diff --git a/src/client/array/dc_array.c b/src/client/array/dc_array.c
index 45b8947b04a..17f2daa80ef 100644
--- a/src/client/array/dc_array.c
+++ b/src/client/array/dc_array.c
@@ -2069,18 +2069,24 @@ free_set_size_cb(tse_task_t *task, void *data)
 }
 
 static int
-punch_extent(daos_handle_t oh, daos_handle_t th, daos_size_t dkey_val, daos_off_t record_i,
-	     daos_size_t num_records, tse_task_t *task, d_list_t *task_list)
+punch_dkey_or_extent(daos_handle_t oh, daos_handle_t th, daos_size_t dkey_val, daos_off_t start,
+		     daos_size_t num_records, bool punch_dkey, tse_task_t *task,
+		     d_list_t *task_list)
 {
 	daos_obj_update_t	*io_arg;
+	daos_obj_punch_t	*dkey_punch_arg;
 	daos_iod_t		*iod;
 	d_sg_list_t		*sgl;
 	daos_key_t		*dkey;
 	struct io_params	*params = NULL;
 	tse_task_t		*io_task = NULL;
-	int			rc;
+	int			 rc;
 
-	D_DEBUG(DB_IO, "Punching (%zu, %zu) in Key %zu\n", record_i + 1, num_records, dkey_val);
+	if (punch_dkey)
+		D_DEBUG(DB_IO, "Punching dkey %zu\n", dkey_val);
+	else
+		D_DEBUG(DB_IO, "Punching (%zu, %zu) in Key %zu\n",
+			start, num_records, dkey_val);
 
 	D_ALLOC_PTR(params);
 	if (params == NULL)
@@ -2094,28 +2100,42 @@ punch_extent(daos_handle_t oh, daos_handle_t th, daos_size_t dkey_val, daos_off_
 	dkey = &params->dkey;
 	d_iov_set(dkey, &params->dkey_val, sizeof(uint64_t));
 
-	/* set descriptor for KV object */
-	d_iov_set(&iod->iod_name, &params->akey_val, 1);
-	iod->iod_nr = 1;
-	iod->iod_size = 0; /* 0 to punch */
-	iod->iod_type = DAOS_IOD_ARRAY;
-	D_ALLOC_PTR(iod->iod_recxs);
-	if (iod->iod_recxs == NULL)
-		D_GOTO(free, rc = -DER_NOMEM);
-	iod->iod_recxs[0].rx_idx = record_i + 1;
-	iod->iod_recxs[0].rx_nr = num_records;
-
-	rc = daos_task_create(DAOS_OPC_OBJ_UPDATE, tse_task2sched(task), 0, NULL, &io_task);
-	if (rc)
-		D_GOTO(free_reqs, rc);
+	if (punch_dkey) {
+		rc = daos_task_create(DAOS_OPC_OBJ_PUNCH_DKEYS, tse_task2sched(task), 0, NULL,
+				      &io_task);
+		if (rc)
+			D_GOTO(free_reqs, rc);
+
+		dkey_punch_arg		= daos_task_get_args(io_task);
+		dkey_punch_arg->oh	= oh;
+		dkey_punch_arg->th	= th;
+		dkey_punch_arg->dkey	= dkey;
+		dkey_punch_arg->akeys	= NULL;
+		dkey_punch_arg->akey_nr	= 0;
+	} else {
+		/* set descriptor for KV object */
+		d_iov_set(&iod->iod_name, &params->akey_val, 1);
+		iod->iod_nr = 1;
+		iod->iod_size = 0; /* 0 to punch */
+		iod->iod_type = DAOS_IOD_ARRAY;
+		D_ALLOC_PTR(iod->iod_recxs);
+		if (iod->iod_recxs == NULL)
+			D_GOTO(free, rc = -DER_NOMEM);
+		iod->iod_recxs[0].rx_idx = start;
+		iod->iod_recxs[0].rx_nr = num_records;
+
+		rc = daos_task_create(DAOS_OPC_OBJ_UPDATE, tse_task2sched(task), 0, NULL, &io_task);
+		if (rc)
+			D_GOTO(free_reqs, rc);
 
-	io_arg = daos_task_get_args(io_task);
-	io_arg->oh	= oh;
-	io_arg->th	= th;
-	io_arg->dkey	= dkey;
-	io_arg->nr	= 1;
-	io_arg->iods	= iod;
-	io_arg->sgls	= sgl;
+		io_arg = daos_task_get_args(io_task);
+		io_arg->oh	= oh;
+		io_arg->th	= th;
+		io_arg->dkey	= dkey;
+		io_arg->nr	= 1;
+		io_arg->iods	= iod;
+		io_arg->sgls	= sgl;
+	}
 
 	rc = tse_task_register_comp_cb(io_task, free_io_params_cb, &params, sizeof(params));
 	if (rc)
@@ -2422,18 +2442,26 @@ adjust_array_size_cb(tse_task_t *task, void *data)
 		memcpy(&dkey_val, ptr, args->kds[i].kd_key_len);
 		ptr += args->kds[i].kd_key_len;
 
+		/*
+		 * Either punch the entire dkey or an extent in that dkey depending on the offset
+		 * where we are truncating to. The first dkey of the array (dkey 1) will always be
+		 * an extent punch to maintain an epoch there.
+		 */
 		if (props->size == 0 || dkey_val > props->dkey_val) {
 			/** Do nothing for DKEY 0 (metadata) */
 			if (dkey_val == 0)
 				continue;
-			/*
-			 * The dkey is higher than the adjustded size so we could punch it here.
-			 * But it's better to punch the extent so that the max_write for the object
-			 * doesn't get lost by aggregation.
-			 */
-			D_DEBUG(DB_IO, "Punch full extent in key "DF_U64"\n", dkey_val);
-			rc = punch_extent(args->oh, args->th, dkey_val, (daos_off_t)-1,
-					  props->chunk_size, props->ptask, &task_list);
+			if (dkey_val == 1) {
+				D_DEBUG(DB_IO, "Punch full extent in key " DF_U64 "\n", dkey_val);
+				rc = punch_dkey_or_extent(args->oh, args->th, dkey_val,
+							  0, props->chunk_size, false,
+							  props->ptask, &task_list);
+			} else {
+				D_DEBUG(DB_IO, "Punch dkey " DF_U64 "\n", dkey_val);
+				rc = punch_dkey_or_extent(args->oh, args->th, dkey_val,
+							  0, props->chunk_size, true,
+							  props->ptask, &task_list);
+			}
 			if (rc)
 				goto out;
 		} else if (dkey_val == props->dkey_val && props->record_i) {
@@ -2444,8 +2472,9 @@ adjust_array_size_cb(tse_task_t *task, void *data)
 					 props->chunk_size);
 				/** Punch all records above record_i */
 				D_DEBUG(DB_IO, "Punch extent in key "DF_U64"\n", dkey_val);
-				rc = punch_extent(args->oh, args->th, dkey_val, props->record_i,
-						  props->num_records, props->ptask, &task_list);
+				rc = punch_dkey_or_extent(args->oh, args->th, dkey_val,
+							  props->record_i + 1, props->num_records,
+							  false, props->ptask, &task_list);
 				if (rc)
 					goto out;
 			}
diff --git a/src/common/pool_map.c b/src/common/pool_map.c
index 7dd83b9603f..2d478778d4a 100644
--- a/src/common/pool_map.c
+++ b/src/common/pool_map.c
@@ -1650,11 +1650,12 @@ gen_pool_buf(struct pool_map *map, struct pool_buf **map_buf_out, int map_versio
 			map_comp.co_flags = PO_COMPF_NONE;
 			map_comp.co_nr = 1;
 
-			D_DEBUG(DB_TRACE, "adding target: type=0x%hhx, status=%hhu, idx=%d, "
+			D_DEBUG(DB_TRACE, "adding target: type=0x%hhx, status=%hhu, idx=%d, id=%d, "
 				"rank=%d, ver=%d, in_ver=%d, fseq=%u, flags=0x%x, nr=%u\n",
 				map_comp.co_type, map_comp.co_status, map_comp.co_index,
-				map_comp.co_rank, map_comp.co_ver, map_comp.co_in_ver,
-				map_comp.co_fseq, map_comp.co_flags, map_comp.co_nr);
+				map_comp.co_id, map_comp.co_rank, map_comp.co_ver,
+				map_comp.co_in_ver, map_comp.co_fseq, map_comp.co_flags,
+				map_comp.co_nr);
 
 			rc = pool_buf_attach(map_buf, &map_comp, 1);
 			if (rc != 0)
diff --git a/src/container/srv_target.c b/src/container/srv_target.c
index 3961f41dcaf..d2c902a2265 100644
--- a/src/container/srv_target.c
+++ b/src/container/srv_target.c
@@ -319,6 +319,7 @@ cont_child_aggregate(struct ds_cont_child *cont, cont_aggregate_cb_t agg_cb,
 
 	if (unlikely(DAOS_FAIL_CHECK(DAOS_FORCE_EC_AGG) ||
 		     DAOS_FAIL_CHECK(DAOS_FORCE_EC_AGG_FAIL) ||
+		     DAOS_FAIL_CHECK(DAOS_OBJ_EC_AGG_LEADER_DIFF) ||
 		     DAOS_FAIL_CHECK(DAOS_FORCE_EC_AGG_PEER_FAIL)))
 		interval = 0;
 	else
@@ -627,13 +628,18 @@ cont_child_alloc_ref(void *co_uuid, unsigned int ksize, void *po_uuid,
 	rc = ABT_cond_create(&cont->sc_scrub_cond);
 	if (rc != ABT_SUCCESS) {
 		rc = dss_abterr2der(rc);
-		goto out_mutex;
+		goto out_resync_cond;
+	}
+	rc = ABT_cond_create(&cont->sc_rebuild_cond);
+	if (rc != ABT_SUCCESS) {
+		rc = dss_abterr2der(rc);
+		goto out_scrub_cond;
 	}
 
 	cont->sc_pool = ds_pool_child_lookup(po_uuid);
 	if (cont->sc_pool == NULL) {
 		rc = -DER_NO_HDL;
-		goto out_cond;
+		goto out_rebuild_cond;
 	}
 
 	rc = vos_cont_open(cont->sc_pool->spc_hdl, co_uuid, &cont->sc_hdl);
@@ -659,7 +665,11 @@ cont_child_alloc_ref(void *co_uuid, unsigned int ksize, void *po_uuid,
 
 out_pool:
 	ds_pool_child_put(cont->sc_pool);
-out_cond:
+out_rebuild_cond:
+	ABT_cond_free(&cont->sc_rebuild_cond);
+out_scrub_cond:
+	ABT_cond_free(&cont->sc_scrub_cond);
+out_resync_cond:
 	ABT_cond_free(&cont->sc_dtx_resync_cond);
 out_mutex:
 	ABT_mutex_free(&cont->sc_mutex);
@@ -686,6 +696,7 @@ cont_child_free_ref(struct daos_llink *llink)
 	D_FREE(cont->sc_snapshots);
 	ABT_cond_free(&cont->sc_dtx_resync_cond);
 	ABT_cond_free(&cont->sc_scrub_cond);
+	ABT_cond_free(&cont->sc_rebuild_cond);
 	ABT_mutex_free(&cont->sc_mutex);
 	D_FREE(cont);
 }
@@ -740,6 +751,12 @@ ds_cont_child_cache_destroy(struct daos_lru_cache *cache)
 	daos_lru_cache_destroy(cache);
 }
 
+static void
+cont_child_put(struct daos_lru_cache *cache, struct ds_cont_child *cont)
+{
+	daos_lru_ref_release(cache, &cont->sc_list);
+}
+
 /*
  * If create == false, then this is assumed to be a pure lookup. In this case,
  * -DER_NONEXIST is returned if the ds_cont_child object does not exist.
@@ -774,12 +791,6 @@ cont_child_lookup(struct daos_lru_cache *cache, const uuid_t co_uuid,
 	return 0;
 }
 
-static void
-cont_child_put(struct daos_lru_cache *cache, struct ds_cont_child *cont)
-{
-	daos_lru_ref_release(cache, &cont->sc_list);
-}
-
 static inline bool
 cont_child_started(struct ds_cont_child *cont_child)
 {
@@ -805,13 +816,17 @@ cont_child_stop(struct ds_cont_child *cont_child)
 	/* Some ds_cont_child will only created by ds_cont_child_lookup().
 	 * never be started at all
 	 */
+	cont_child->sc_stopping = 1;
+
+	/* Stop DTX reindex by force. */
+	stop_dtx_reindex_ult(cont_child, true);
+
 	if (cont_child_started(cont_child)) {
 		D_DEBUG(DB_MD, DF_CONT"[%d]: Stopping container\n",
 			DP_CONT(cont_child->sc_pool->spc_uuid,
 				cont_child->sc_uuid),
 			dss_get_module_info()->dmi_tgt_id);
 
-		cont_child->sc_stopping = 1;
 		d_list_del_init(&cont_child->sc_link);
 
 		dtx_cont_deregister(cont_child);
@@ -1164,6 +1179,7 @@ cont_child_destroy_one(void *vin)
 				       &cont);
 		if (rc == -DER_NONEXIST)
 			break;
+
 		if (rc != 0)
 			D_GOTO(out_pool, rc);
 
@@ -1187,10 +1203,6 @@ cont_child_destroy_one(void *vin)
 			ABT_cond_wait(cont->sc_dtx_resync_cond, cont->sc_mutex);
 		ABT_mutex_unlock(cont->sc_mutex);
 
-		/* Give chance to DTX reindex ULT for exit. */
-		if (unlikely(cont->sc_dtx_reindex))
-			ABT_thread_yield();
-
 		/* Make sure checksum scrubbing has stopped */
 		ABT_mutex_lock(cont->sc_mutex);
 		if (cont->sc_scrubbing) {
@@ -1199,6 +1211,12 @@ cont_child_destroy_one(void *vin)
 		}
 		ABT_mutex_unlock(cont->sc_mutex);
 
+		/* Make sure rebuild has stopped */
+		ABT_mutex_lock(cont->sc_mutex);
+		if (cont->sc_rebuilding)
+			ABT_cond_wait(cont->sc_rebuild_cond, cont->sc_mutex);
+		ABT_mutex_unlock(cont->sc_mutex);
+
 		retry_cnt++;
 		if (retry_cnt > 1) {
 			D_ERROR("container is still in-use: open %u, resync %s, reindex %s\n",
@@ -1300,9 +1318,20 @@ ds_cont_child_lookup(uuid_t pool_uuid, uuid_t cont_uuid,
 		     struct ds_cont_child **ds_cont)
 {
 	struct dsm_tls		*tls = dsm_tls_get();
+	int			 rc;
+
+	rc = cont_child_lookup(tls->dt_cont_cache, cont_uuid, pool_uuid,
+			       true /* create */, ds_cont);
+	if (rc != 0)
+		return rc;
 
-	return cont_child_lookup(tls->dt_cont_cache, cont_uuid, pool_uuid,
-				 true /* create */, ds_cont);
+	if ((*ds_cont)->sc_stopping) {
+		cont_child_put(tls->dt_cont_cache, *ds_cont);
+		*ds_cont = NULL;
+		return -DER_SHUTDOWN;
+	}
+
+	return 0;
 }
 
 /**
@@ -1572,7 +1601,7 @@ ds_cont_local_open(uuid_t pool_uuid, uuid_t cont_hdl_uuid, uuid_t cont_uuid,
 		  DF_UUID": %d\n", DP_UUID(cont_uuid), hdl->sch_cont->sc_open);
 
 	hdl->sch_cont->sc_open--;
-	dtx_cont_close(hdl->sch_cont);
+	dtx_cont_close(hdl->sch_cont, true);
 
 err_cont:
 	if (daos_handle_is_valid(poh)) {
@@ -1694,7 +1723,7 @@ cont_close_hdl(uuid_t cont_hdl_uuid)
 		D_ASSERT(cont_child->sc_open > 0);
 		cont_child->sc_open--;
 		if (cont_child->sc_open == 0)
-			dtx_cont_close(cont_child);
+			dtx_cont_close(cont_child, false);
 
 		D_DEBUG(DB_MD, DF_CONT": closed (%d): hdl="DF_UUID"\n",
 			DP_CONT(cont_child->sc_pool->spc_uuid, cont_child->sc_uuid),
diff --git a/src/dtx/dtx_common.c b/src/dtx/dtx_common.c
index ee119d4b965..c6ce2f38206 100644
--- a/src/dtx/dtx_common.c
+++ b/src/dtx/dtx_common.c
@@ -1635,6 +1635,10 @@ start_dtx_reindex_ult(struct ds_cont_child *cont)
 	while (cont->sc_dtx_reindex_abort)
 		ABT_thread_yield();
 
+	if (cont->sc_stopping)
+		return -DER_SHUTDOWN;
+
+	cont->sc_dtx_delay_reset = 0;
 	if (cont->sc_dtx_reindex)
 		return 0;
 
@@ -1652,7 +1656,7 @@ start_dtx_reindex_ult(struct ds_cont_child *cont)
 }
 
 void
-stop_dtx_reindex_ult(struct ds_cont_child *cont)
+stop_dtx_reindex_ult(struct ds_cont_child *cont, bool force)
 {
 	/* DTX reindex has been done or not has not been started. */
 	if (!cont->sc_dtx_reindex)
@@ -1662,9 +1666,15 @@ stop_dtx_reindex_ult(struct ds_cont_child *cont)
 	if (dtx_cont_opened(cont))
 		return;
 
-	/* Do not stop DTX reindex if DTX resync is still in-progress. */
-	if (cont->sc_dtx_resyncing)
+	/*
+	 * For non-force case, do not stop DTX re-index if DTX resync
+	 * is in-progress. Related DTX resource will be released after
+	 * DTX resync globally done (via rebuild scanning).
+	 */
+	if (unlikely(cont->sc_dtx_resyncing && !force)) {
+		cont->sc_dtx_delay_reset = 1;
 		return;
+	}
 
 	cont->sc_dtx_reindex_abort = 1;
 
@@ -1822,7 +1832,7 @@ dtx_cont_open(struct ds_cont_child *cont)
 }
 
 void
-dtx_cont_close(struct ds_cont_child *cont)
+dtx_cont_close(struct ds_cont_child *cont, bool force)
 {
 	struct dss_module_info		*dmi = dss_get_module_info();
 	struct dtx_batched_pool_args	*dbpa;
@@ -1837,7 +1847,7 @@ dtx_cont_close(struct ds_cont_child *cont)
 
 		d_list_for_each_entry(dbca, &dbpa->dbpa_cont_list, dbca_pool_link) {
 			if (dbca->dbca_cont == cont) {
-				stop_dtx_reindex_ult(cont);
+				stop_dtx_reindex_ult(cont, force);
 				d_list_del(&dbca->dbca_sys_link);
 				d_list_add_tail(&dbca->dbca_sys_link,
 						&dmi->dmi_dtx_batched_cont_close_list);
@@ -1845,8 +1855,12 @@ dtx_cont_close(struct ds_cont_child *cont)
 
 				/* If nobody reopen the container during dtx_flush_on_close,
 				 * then reset DTX table in VOS to release related resources.
+				 *
+				 * For non-force case, do not reset DTX table if DTX resync
+				 * is in-progress to avoid redoing DTX re-index. We will do
+				 * that after DTX resync done globally.
 				 */
-				if (!dtx_cont_opened(cont))
+				if (likely(!dtx_cont_opened(cont) && cont->sc_dtx_delay_reset == 0))
 					vos_dtx_cache_reset(cont->sc_hdl, false);
 				return;
 			}
diff --git a/src/dtx/dtx_internal.h b/src/dtx/dtx_internal.h
index 70509e25a5c..04f7c3f617e 100644
--- a/src/dtx/dtx_internal.h
+++ b/src/dtx/dtx_internal.h
@@ -195,7 +195,6 @@ int dtx_handle_reinit(struct dtx_handle *dth);
 void dtx_batched_commit(void *arg);
 void dtx_aggregation_main(void *arg);
 int start_dtx_reindex_ult(struct ds_cont_child *cont);
-void stop_dtx_reindex_ult(struct ds_cont_child *cont);
 
 /* dtx_cos.c */
 int dtx_fetch_committable(struct ds_cont_child *cont, uint32_t max_cnt,
diff --git a/src/dtx/dtx_resync.c b/src/dtx/dtx_resync.c
index 3a598a7da2e..82e72c81586 100644
--- a/src/dtx/dtx_resync.c
+++ b/src/dtx/dtx_resync.c
@@ -1,5 +1,5 @@
 /**
- * (C) Copyright 2019-2023 Intel Corporation.
+ * (C) Copyright 2019-2024 Intel Corporation.
  *
  * SPDX-License-Identifier: BSD-2-Clause-Patent
  */
@@ -704,9 +704,6 @@ dtx_resync(daos_handle_t po_hdl, uuid_t po_uuid, uuid_t co_uuid, uint32_t ver, b
 	ABT_mutex_unlock(cont->sc_mutex);
 
 out:
-	if (!dtx_cont_opened(cont))
-		stop_dtx_reindex_ult(cont);
-
 	D_DEBUG(DB_MD, "Exit DTX resync (%s) for "DF_UUID"/"DF_UUID" with ver %u, rc = %d\n",
 		block ? "block" : "non-block", DP_UUID(po_uuid), DP_UUID(co_uuid), ver, rc);
 
@@ -751,8 +748,8 @@ dtx_resync_one(void *data)
 {
 	struct dtx_scan_args		*arg = data;
 	struct ds_pool_child		*child;
-	vos_iter_param_t		 param = { 0 };
-	struct vos_iter_anchors		 anchor = { 0 };
+	vos_iter_param_t		*param = NULL;
+	struct vos_iter_anchors		*anchor = NULL;
 	struct dtx_container_scan_arg	 cb_arg = { 0 };
 	int				 rc;
 
@@ -760,14 +757,26 @@ dtx_resync_one(void *data)
 	if (child == NULL)
 		D_GOTO(out, rc = -DER_NONEXIST);
 
+	D_ALLOC_PTR(param);
+	if (param == NULL)
+		D_GOTO(out, rc = -DER_NOMEM);
+
+	D_ALLOC_PTR(anchor);
+	if (anchor == NULL)
+		D_GOTO(out, rc = -DER_NOMEM);
+
 	cb_arg.arg = *arg;
-	param.ip_hdl = child->spc_hdl;
-	param.ip_flags = VOS_IT_FOR_MIGRATION;
-	rc = vos_iterate(&param, VOS_ITER_COUUID, false, &anchor,
+	param->ip_hdl = child->spc_hdl;
+	param->ip_flags = VOS_IT_FOR_MIGRATION;
+	rc = vos_iterate(param, VOS_ITER_COUUID, false, anchor,
 			 container_scan_cb, NULL, &cb_arg, NULL);
 
-	ds_pool_child_put(child);
 out:
+	D_FREE(param);
+	D_FREE(anchor);
+	if (child != NULL)
+		ds_pool_child_put(child);
+
 	D_DEBUG(DB_TRACE, DF_UUID" iterate pool done: rc %d\n",
 		DP_UUID(arg->pool_uuid), rc);
 
diff --git a/src/include/daos/common.h b/src/include/daos/common.h
index c46ce5680b8..6a68642d7fc 100644
--- a/src/include/daos/common.h
+++ b/src/include/daos/common.h
@@ -829,6 +829,7 @@ enum {
 #define DAOS_SHARD_OBJ_RW_DROP_REPLY (DAOS_FAIL_SYS_TEST_GROUP_LOC | 0x80)
 #define DAOS_OBJ_FETCH_DATA_LOST	(DAOS_FAIL_SYS_TEST_GROUP_LOC | 0x81)
 #define DAOS_OBJ_TRY_SPECIAL_SHARD	(DAOS_FAIL_SYS_TEST_GROUP_LOC | 0x82)
+#define DAOS_OBJ_EC_AGG_LEADER_DIFF	(DAOS_FAIL_SYS_TEST_GROUP_LOC | 0x83)
 
 #define DAOS_VOS_AGG_RANDOM_YIELD	(DAOS_FAIL_UNIT_TEST_GROUP_LOC | 0x90)
 #define DAOS_VOS_AGG_MW_THRESH		(DAOS_FAIL_UNIT_TEST_GROUP_LOC | 0x91)
diff --git a/src/include/daos_srv/container.h b/src/include/daos_srv/container.h
index 10feb7e07e3..86310f0bbd7 100644
--- a/src/include/daos_srv/container.h
+++ b/src/include/daos_srv/container.h
@@ -1,5 +1,5 @@
 /*
- * (C) Copyright 2015-2023 Intel Corporation.
+ * (C) Copyright 2015-2024 Intel Corporation.
  *
  * SPDX-License-Identifier: BSD-2-Clause-Patent
  */
@@ -64,15 +64,18 @@ struct ds_cont_child {
 	ABT_mutex		 sc_mutex;
 	ABT_cond		 sc_dtx_resync_cond;
 	ABT_cond		 sc_scrub_cond;
+	ABT_cond		 sc_rebuild_cond;
 	uint32_t		 sc_dtx_resyncing:1,
 				 sc_dtx_reindex:1,
 				 sc_dtx_reindex_abort:1,
+				 sc_dtx_delay_reset:1,
 				 sc_dtx_registered:1,
 				 sc_props_fetched:1,
 				 sc_stopping:1,
 				 sc_vos_agg_active:1,
 				 sc_ec_agg_active:1,
-				 sc_scrubbing:1;
+				 sc_scrubbing:1,
+				 sc_rebuilding:1;
 	uint32_t		 sc_dtx_batched_gen;
 	/* Tracks the schedule request for aggregation ULT */
 	struct sched_request	*sc_agg_req;
diff --git a/src/include/daos_srv/dtx_srv.h b/src/include/daos_srv/dtx_srv.h
index 7e3b1a67946..cee99e4fbd6 100644
--- a/src/include/daos_srv/dtx_srv.h
+++ b/src/include/daos_srv/dtx_srv.h
@@ -252,12 +252,14 @@ dtx_leader_exec_ops(struct dtx_leader_handle *dlh, dtx_sub_func_t func,
 
 int dtx_cont_open(struct ds_cont_child *cont);
 
-void dtx_cont_close(struct ds_cont_child *cont);
+void dtx_cont_close(struct ds_cont_child *cont, bool force);
 
 int dtx_cont_register(struct ds_cont_child *cont);
 
 void dtx_cont_deregister(struct ds_cont_child *cont);
 
+void stop_dtx_reindex_ult(struct ds_cont_child *cont, bool force);
+
 int dtx_obj_sync(struct ds_cont_child *cont, daos_unit_oid_t *oid,
 		 daos_epoch_t epoch);
 
diff --git a/src/object/srv_ec_aggregate.c b/src/object/srv_ec_aggregate.c
index c73def48a8d..38fd8c0a496 100644
--- a/src/object/srv_ec_aggregate.c
+++ b/src/object/srv_ec_aggregate.c
@@ -115,7 +115,8 @@ struct ec_agg_entry {
 	struct pl_obj_layout	*ae_obj_layout;
 	struct daos_shard_loc	 ae_peer_pshards[OBJ_EC_MAX_P];
 	uint32_t		 ae_grp_idx;
-	uint32_t		ae_is_leader:1;
+	uint32_t		ae_is_leader:1,
+				ae_process_partial:1;
 };
 
 /* Parameters used to drive iterate all.
@@ -148,6 +149,7 @@ struct ec_agg_stripe_ud {
 	d_iov_t			 asu_csum_iov;
 	struct dcs_iod_csums	*asu_iod_csums; /* iod csums */
 	ABT_eventual		 asu_eventual;  /* Eventual for offload  */
+	bool			 asu_valid_hole; /* with hole epoch >= parity epoch */
 };
 
 /* Represents an replicated data extent.
@@ -500,26 +502,28 @@ agg_count_cells(uint8_t *fcbit_map, uint8_t *tbit_map, uint64_t estart,
  * initialized and share to other servers at higher(pool/container) layer.
  */
 static int
-agg_get_obj_handle(struct ec_agg_entry *entry)
+agg_get_obj_handle(struct ec_agg_entry *entry, bool reset_peer)
 {
 	struct ec_agg_param	*agg_param;
 	uint32_t		grp_start;
 	uint32_t		tgt_ec_idx;
 	struct dc_object	*obj;
 	int			i;
-	int			rc;
+	int			rc = 0;
 
-	if (daos_handle_is_valid(entry->ae_obj_hdl))
+	if (daos_handle_is_valid(entry->ae_obj_hdl) && !reset_peer)
 		return 0;
 
 	agg_param = container_of(entry, struct ec_agg_param, ap_agg_entry);
-	rc = dsc_obj_open(agg_param->ap_pool_info.api_cont_hdl,
-			  entry->ae_oid.id_pub, DAOS_OO_RW,
-			  &entry->ae_obj_hdl);
-	if (rc)
-		goto out;
+	if (!daos_handle_is_valid(entry->ae_obj_hdl)) {
+		rc = dsc_obj_open(agg_param->ap_pool_info.api_cont_hdl,
+				  entry->ae_oid.id_pub, DAOS_OO_RW,
+				  &entry->ae_obj_hdl);
+		if (rc)
+			goto out;
+	}
 
-	if (entry->ae_peer_pshards[0].sd_rank != DAOS_TGT_IGNORE)
+	if (!reset_peer && entry->ae_peer_pshards[0].sd_rank != DAOS_TGT_IGNORE)
 		D_GOTO(out, rc = 0);
 
 	grp_start = entry->ae_grp_idx * entry->ae_obj_layout->ol_grp_size;
@@ -599,7 +603,7 @@ agg_fetch_odata_cells(struct ec_agg_entry *entry, uint8_t *bit_map,
 	for (i = 0; i < cell_cnt; i++)
 		d_iov_set(&sgl.sg_iovs[i], &buf[i * cell_b], cell_b);
 
-	rc = agg_get_obj_handle(entry);
+	rc = agg_get_obj_handle(entry, false);
 	if (rc) {
 		D_ERROR("Failed to open object: "DF_RC"\n", DP_RC(rc));
 		goto out;
@@ -1180,7 +1184,13 @@ agg_process_partial_stripe(struct ec_agg_entry *entry)
 	estart = entry->ae_cur_stripe.as_offset;
 	d_list_for_each_entry(extent, &entry->ae_cur_stripe.as_dextents,
 			      ae_link) {
-		D_ASSERT(!extent->ae_hole);
+		if (extent->ae_hole) {
+			/* valid hole processed by agg_process_holes_ult() */
+			D_ASSERTF(extent->ae_epoch < entry->ae_par_extent.ape_epoch,
+				  "hole ext epoch "DF_X64", parity epoch "DF_X64"\n",
+				  extent->ae_epoch, entry->ae_par_extent.ape_epoch);
+			continue;
+		}
 		if (extent->ae_epoch <= entry->ae_par_extent.ape_epoch) {
 			has_old_replicas = true;
 			continue;
@@ -1311,9 +1321,9 @@ agg_peer_update_ult(void *arg)
 		rc = obj_req_create(dss_get_module_info()->dmi_ctx, &tgt_ep,
 				    DAOS_OBJ_RPC_EC_AGGREGATE, &rpc);
 		if (rc) {
-			D_ERROR(DF_UOID" pidx %d to peer %d, obj_req_create "
+			D_ERROR(DF_UOID" pidx %d to peer %d, rank %d tag %d obj_req_create "
 				DF_RC"\n", DP_UOID(entry->ae_oid), pidx, peer,
-				DP_RC(rc));
+				tgt_ep.ep_rank, tgt_ep.ep_tag, DP_RC(rc));
 			goto out;
 		}
 		ec_agg_in = crt_req_get(rpc);
@@ -1448,7 +1458,7 @@ agg_peer_update(struct ec_agg_entry *entry, bool write_parity)
 		return -1;
 	}
 
-	rc = agg_get_obj_handle(entry);
+	rc = agg_get_obj_handle(entry, false);
 	if (rc) {
 		D_ERROR("Failed to open object: "DF_RC"\n", DP_RC(rc));
 		return rc;
@@ -1536,8 +1546,8 @@ agg_process_holes_ult(void *arg)
 	uint32_t		 pidx = ec_age2pidx(entry);
 	uint32_t		 peer;
 	int			 i, rc = 0;
-	bool			 valid_hole = false;
 
+	stripe_ud->asu_valid_hole = false;
 	/* Process extent list to find what to re-replicate -- build recx array
 	 */
 	d_list_for_each_entry(agg_extent,
@@ -1545,7 +1555,7 @@ agg_process_holes_ult(void *arg)
 		if (agg_extent->ae_epoch < entry->ae_par_extent.ape_epoch)
 			continue;
 		if (agg_extent->ae_hole)
-			valid_hole = true;
+			stripe_ud->asu_valid_hole = true;
 		if (agg_extent->ae_recx.rx_idx - ss > last_ext_end) {
 			stripe_ud->asu_recxs[ext_cnt].rx_idx =
 				ss + last_ext_end;
@@ -1561,7 +1571,7 @@ agg_process_holes_ult(void *arg)
 			break;
 	}
 
-	if (!valid_hole)
+	if (!stripe_ud->asu_valid_hole)
 		goto out;
 
 	obj = obj_hdl2ptr(entry->ae_obj_hdl);
@@ -1731,7 +1741,7 @@ agg_process_holes(struct ec_agg_entry *entry)
 	}
 
 	stripe_ud.asu_agg_entry = entry;
-	rc = agg_get_obj_handle(entry);
+	rc = agg_get_obj_handle(entry, false);
 	if (rc) {
 		D_ERROR("Failed to open object: "DF_RC"\n", DP_RC(rc));
 		goto out;
@@ -1758,21 +1768,29 @@ agg_process_holes(struct ec_agg_entry *entry)
 	if (*status != 0)
 		D_GOTO(ev_out, rc = *status);
 
-	/* Update local vos with replicate */
-	entry->ae_sgl.sg_nr = 1;
-	if (iod->iod_nr) {
-		/* write the reps to vos */
-		rc = vos_obj_update(agg_param->ap_cont_handle, entry->ae_oid,
-				    entry->ae_cur_stripe.as_hi_epoch, 0, 0,
-				    &entry->ae_dkey, 1, iod,
-				    stripe_ud.asu_iod_csums,
-				    &entry->ae_sgl);
-		if (rc) {
-			D_ERROR("vos_update_begin failed: "DF_RC"\n",
-				DP_RC(rc));
-			goto ev_out;
+	/* If with valid hole (hole epoch >= parity epoch), update local vos with replicas
+	 * and delete parity.
+	 * For the case without valid hole, the only possibility is with partial replica epoch >
+	 * parity epoch, and all hole epoch < parity epoch, this case set ae_process_partial
+	 * flag and will call agg_process_partial_stripe() later.
+	 */
+	if (stripe_ud.asu_valid_hole) {
+		if (iod->iod_nr) {
+			/* write the reps to vos */
+			entry->ae_sgl.sg_nr = 1;
+			rc = vos_obj_update(agg_param->ap_cont_handle, entry->ae_oid,
+					    entry->ae_cur_stripe.as_hi_epoch, 0, 0,
+					    &entry->ae_dkey, 1, iod,
+					    stripe_ud.asu_iod_csums,
+					    &entry->ae_sgl);
+			if (rc) {
+				D_ERROR("vos_update_begin failed: "DF_RC"\n",
+					DP_RC(rc));
+				goto ev_out;
+			}
 		}
-		/* Delete parity */
+
+		/* Delete parity even when nothing to replicate */
 		epoch_range.epr_lo = agg_param->ap_epr.epr_lo;
 		epoch_range.epr_hi = entry->ae_cur_stripe.as_hi_epoch;
 		recx.rx_nr = ec_age2cs(entry);
@@ -1782,7 +1800,11 @@ agg_process_holes(struct ec_agg_entry *entry)
 					  entry->ae_oid, &epoch_range,
 					  &entry->ae_dkey, &entry->ae_akey,
 					  &recx);
+	} else {
+		D_DEBUG(DB_EPC, "no valid hole, set ae_process_partial flag\n");
+		entry->ae_process_partial = 1;
 	}
+
 ev_out:
 	entry->ae_sgl.sg_nr = AGG_IOV_CNT;
 	ABT_eventual_free(&stripe_ud.asu_eventual);
@@ -1792,6 +1814,7 @@ agg_process_holes(struct ec_agg_entry *entry)
 	daos_csummer_free_ic(stripe_ud.asu_csummer, &stripe_ud.asu_iod_csums);
 	D_FREE(stripe_ud.asu_csum_iov.iov_buf);
 	daos_csummer_destroy(&stripe_ud.asu_csummer);
+
 	return rc;
 }
 
@@ -1805,7 +1828,6 @@ agg_process_stripe(struct ec_agg_param *agg_param, struct ec_agg_entry *entry)
 	struct vos_iter_anchors	anchors = { 0 };
 	bool			update_vos = true;
 	bool			write_parity = true;
-	bool			process_holes = false;
 	int			rc = 0;
 
 	if (DAOS_FAIL_CHECK(DAOS_FORCE_EC_AGG_FAIL))
@@ -1876,16 +1898,23 @@ agg_process_stripe(struct ec_agg_param *agg_param, struct ec_agg_entry *entry)
 		goto out;
 	}
 
-	/* With parity and some newer partial replicas, possibly holes */
-	if (ec_age_with_hole(entry))
-		process_holes = true;
-	else
-		rc = agg_process_partial_stripe(entry);
+	/* With parity and some newer partial replicas, possibly holes.
+	 * Case 1: with valid hole (hole epoch >= parity epoch), can be handled by
+	 *         agg_process_holes().
+	 * Case 2: without valid hole, must with partial replica, should be handled by
+	 *         agg_process_partial_stripe().
+	 */
+	if (ec_age_with_hole(entry)) {
+		entry->ae_process_partial = 0;
+		rc = agg_process_holes(entry);
+		if (rc != 0 || !entry->ae_process_partial)
+			goto clear_exts;
+	}
+
+	rc = agg_process_partial_stripe(entry);
 
 out:
-	if (process_holes && rc == 0) {
-		rc = agg_process_holes(entry);
-	} else if (update_vos && rc == 0) {
+	if (update_vos && rc == 0) {
 		if (ec_age2p(entry) > 1)  {
 			/* offload of ds_obj_update to push remote parity */
 			rc = agg_peer_update(entry, write_parity);
@@ -1902,6 +1931,7 @@ agg_process_stripe(struct ec_agg_param *agg_param, struct ec_agg_entry *entry)
 		}
 	}
 
+clear_exts:
 	agg_clear_extents(entry);
 	return rc;
 }
@@ -2113,9 +2143,16 @@ agg_shard_is_parity(struct ds_pool *pool, struct ec_agg_entry *agg_entry)
 		uint32_t shard_idx;
 		struct pl_obj_shard *shard;
 
-		ec_tgt_idx = obj_ec_shard_idx_by_layout_ver(agg_entry->ae_oid.id_layout_ver,
-							    agg_entry->ae_dkey_hash, oca,
-							    daos_oclass_grp_size(oca) - i - 1);
+		if (unlikely(DAOS_FAIL_CHECK(DAOS_OBJ_EC_AGG_LEADER_DIFF) &&
+			     agg_entry->ae_dkey_hash % obj_ec_parity_tgt_nr(oca) == 0))
+			ec_tgt_idx = obj_ec_shard_idx_by_layout_ver(agg_entry->ae_oid.id_layout_ver,
+								    agg_entry->ae_dkey_hash, oca,
+								    obj_ec_data_tgt_nr(oca) + i);
+		else
+			ec_tgt_idx = obj_ec_shard_idx_by_layout_ver(agg_entry->ae_oid.id_layout_ver,
+								    agg_entry->ae_dkey_hash, oca,
+								    daos_oclass_grp_size(oca)
+								    - i - 1);
 
 		shard_idx = grp_start + ec_tgt_idx;
 		shard = pl_obj_get_shard(agg_entry->ae_obj_layout, shard_idx);
@@ -2162,6 +2199,8 @@ agg_dkey(daos_handle_t ih, vos_iter_entry_t *entry,
 	 struct ec_agg_param *agg_param, struct ec_agg_entry *agg_entry,
 	 unsigned int *acts)
 {
+	int	rc = 0;
+
 	if (!agg_key_compare(agg_entry->ae_dkey, entry->ie_key)) {
 		D_DEBUG(DB_EPC, "Skip dkey: "DF_KEY" ec agg on re-probe\n",
 			DP_KEY(&entry->ie_key));
@@ -2180,11 +2219,12 @@ agg_dkey(daos_handle_t ih, vos_iter_entry_t *entry,
 			DP_UOID(agg_entry->ae_oid), DP_KEY(&agg_entry->ae_dkey),
 			agg_entry->ae_is_leader ? "yes" : "no");
 		agg_reset_dkey_entry(&agg_param->ap_agg_entry, entry);
+		rc = agg_get_obj_handle(agg_entry, true);
 	} else {
 		*acts |= VOS_ITER_CB_SKIP;
 	}
 
-	return 0;
+	return rc;
 }
 
 /* Handles akeys returned by the iterator. */
diff --git a/src/object/srv_obj.c b/src/object/srv_obj.c
index 11a26749695..deadc5f0474 100644
--- a/src/object/srv_obj.c
+++ b/src/object/srv_obj.c
@@ -2478,6 +2478,8 @@ ds_obj_ec_rep_handler(crt_rpc_t *rpc)
 	D_ASSERT(ioc.ioc_coc != NULL);
 	dkey = (daos_key_t *)&oer->er_dkey;
 	iod = (daos_iod_t *)&oer->er_iod;
+	if (iod->iod_nr == 0) /* nothing to replicate, directly remove parity */
+		goto remove_parity;
 	iod_csums = oer->er_iod_csums.ca_arrays;
 	rc        = vos_update_begin(ioc.ioc_coc->sc_hdl, oer->er_oid, oer->er_epoch_range.epr_hi,
 				     VOS_OF_REBUILD, dkey, 1, iod, iod_csums, 0, &ioh, NULL);
@@ -2510,6 +2512,7 @@ ds_obj_ec_rep_handler(crt_rpc_t *rpc)
 			DP_RC(rc));
 		goto out;
 	}
+remove_parity:
 	recx.rx_nr = obj_ioc2ec_cs(&ioc);
 	recx.rx_idx = (oer->er_stripenum * recx.rx_nr) | PARITY_INDICATOR;
 	rc = vos_obj_array_remove(ioc.ioc_coc->sc_hdl, oer->er_oid, &oer->er_epoch_range, dkey,
diff --git a/src/object/srv_obj_migrate.c b/src/object/srv_obj_migrate.c
index 7725e60fd1f..3785ae3daee 100644
--- a/src/object/srv_obj_migrate.c
+++ b/src/object/srv_obj_migrate.c
@@ -1657,6 +1657,12 @@ migrate_punch(struct migrate_pool_tls *tls, struct migrate_one *mrone,
 
 	/* punch records */
 	if (mrone->mo_punch_iod_num > 0 && mrone->mo_rec_punch_eph <= tls->mpt_max_eph) {
+		if (daos_oclass_is_ec(&mrone->mo_oca) &&
+		    !is_ec_parity_shard_by_layout_ver(mrone->mo_oid.id_layout_ver,
+						      mrone->mo_dkey_hash, &mrone->mo_oca,
+						      mrone->mo_oid.id_shard))
+			mrone_recx_daos2_vos(mrone, mrone->mo_punch_iods, mrone->mo_punch_iod_num);
+
 		rc = vos_obj_update(cont->sc_hdl, mrone->mo_oid,
 				    mrone->mo_rec_punch_eph,
 				    mrone->mo_version, 0, &mrone->mo_dkey,
@@ -2351,7 +2357,7 @@ punch_iod_pack(struct migrate_one *mrone, struct dc_object *obj, daos_iod_t *iod
 
 	D_DEBUG(DB_TRACE,
 		"idx %d akey "DF_KEY" nr %d size "DF_U64" type %d\n",
-		idx, DP_KEY(&iod->iod_name), iod->iod_nr, iod->iod_size,
+		idx, DP_KEY(&iod->iod_name), mrone->mo_punch_iods->iod_nr, iod->iod_size,
 		iod->iod_type);
 
 	if (mrone->mo_rec_punch_eph < eph)
diff --git a/src/rebuild/rebuild_internal.h b/src/rebuild/rebuild_internal.h
index 7615a86d777..42c40f81430 100644
--- a/src/rebuild/rebuild_internal.h
+++ b/src/rebuild/rebuild_internal.h
@@ -1,5 +1,5 @@
 /**
- * (C) Copyright 2017-2023 Intel Corporation.
+ * (C) Copyright 2017-2024 Intel Corporation.
  *
  * SPDX-License-Identifier: BSD-2-Clause-Patent
  */
@@ -175,7 +175,10 @@ struct rebuild_status_completed {
 /* Structure on all targets to track all pool rebuilding */
 struct rebuild_global {
 	/* Link rebuild_tgt_pool_tracker on all targets.
-	 * Only operated by stream 0, no need lock.
+	 * Can be inserted/deleted by system XS, be lookup by system XS or VOS target main XS.
+	 * Be protected by rg_ttl_rwlock -
+	 * system XS takes wrlock to insert/delete, VOS TGT XS takes rdlock to lookup,
+	 * no lock needed for system XS to lookup.
 	 */
 	d_list_t	rg_tgt_tracker_list;
 
@@ -200,6 +203,9 @@ struct rebuild_global {
 	 */
 	d_list_t	rg_queue_list;
 
+	/* rwlock to protect rg_tgt_tracker_list */
+	ABT_rwlock	rg_ttl_rwlock;
+
 	ABT_mutex	rg_lock;
 	ABT_cond	rg_stop_cond;
 	/* how many pools is being rebuilt */
@@ -306,6 +312,7 @@ rebuild_tls_get()
 
 void rpt_get(struct rebuild_tgt_pool_tracker *rpt);
 void rpt_put(struct rebuild_tgt_pool_tracker *rpt);
+void rpt_delete(struct rebuild_tgt_pool_tracker *rpt);
 
 struct rebuild_pool_tls *
 rebuild_pool_tls_lookup(uuid_t pool_uuid, unsigned int ver, uint32_t gen);
diff --git a/src/rebuild/scan.c b/src/rebuild/scan.c
index 8778292e346..39f79f29b33 100644
--- a/src/rebuild/scan.c
+++ b/src/rebuild/scan.c
@@ -1,5 +1,5 @@
 /**
- * (C) Copyright 2017-2023 Intel Corporation.
+ * (C) Copyright 2017-2024 Intel Corporation.
  *
  * SPDX-License-Identifier: BSD-2-Clause-Patent
  */
@@ -393,6 +393,7 @@ struct rebuild_scan_arg {
 	int				snapshot_cnt;
 	uint32_t			yield_freq;
 	int32_t				obj_yield_cnt;
+	struct ds_cont_child		*cont_child;
 };
 
 /**
@@ -668,7 +669,7 @@ rebuild_obj_scan_cb(daos_handle_t ch, vos_iter_entry_t *ent,
 	int				i;
 	int				rc = 0;
 
-	if (rpt->rt_abort) {
+	if (rpt->rt_abort || arg->cont_child->sc_stopping) {
 		D_DEBUG(DB_REBUILD, "rebuild is aborted\n");
 		return 1;
 	}
@@ -806,44 +807,66 @@ rebuild_container_scan_cb(daos_handle_t ih, vos_iter_entry_t *entry,
 	}
 
 	rc = vos_cont_open(iter_param->ip_hdl, entry->ie_couuid, &coh);
+	if (rc == -DER_NONEXIST) {
+		D_DEBUG(DB_REBUILD, DF_UUID" already destroyed\n", DP_UUID(arg->co_uuid));
+		return 0;
+	}
+
 	if (rc != 0) {
 		D_ERROR("Open container "DF_UUID" failed: "DF_RC"\n",
 			DP_UUID(entry->ie_couuid), DP_RC(rc));
 		return rc;
 	}
 
+	rc = ds_cont_child_lookup(rpt->rt_pool_uuid, entry->ie_couuid, &cont_child);
+	if (rc == -DER_NONEXIST || rc == -DER_SHUTDOWN) {
+		D_DEBUG(DB_REBUILD, DF_UUID" already destroyed or destroying\n",
+			DP_UUID(arg->co_uuid));
+		rc = 0;
+		D_GOTO(close, rc);
+	}
+
+	if (rc != 0) {
+		D_ERROR("Container "DF_UUID", ds_cont_child_lookup failed: "DF_RC"\n",
+			DP_UUID(entry->ie_couuid), DP_RC(rc));
+		D_GOTO(close, rc);
+	}
+
+	/*
+	 * The container may has been closed by the application, but some resource (DRAM) occupied
+	 * by DTX may be not released because DTX resync was in-progress at that time. When arrive
+	 * here, DTX resync must has completed globally. Let's release related resource.
+	 */
+	if (unlikely(cont_child->sc_dtx_delay_reset == 1)) {
+		stop_dtx_reindex_ult(cont_child, true);
+		vos_dtx_cache_reset(cont_child->sc_hdl, false);
+	}
+
+	cont_child->sc_rebuilding = 1;
+
 	rc = ds_cont_fetch_snaps(rpt->rt_pool->sp_iv_ns, entry->ie_couuid, NULL,
 				 &snapshot_cnt);
 	if (rc) {
 		D_ERROR("Container "DF_UUID", ds_cont_fetch_snaps failed: "DF_RC"\n",
 			DP_UUID(entry->ie_couuid), DP_RC(rc));
-		vos_cont_close(coh);
-		return rc;
+		D_GOTO(close, rc);
 	}
 
 	rc = ds_cont_get_props(&arg->co_props, rpt->rt_pool->sp_uuid, entry->ie_couuid);
 	if (rc) {
 		D_ERROR("Container "DF_UUID", ds_cont_get_props failed: "DF_RC"\n",
 			DP_UUID(entry->ie_couuid), DP_RC(rc));
-		vos_cont_close(coh);
-		return rc;
-	}
-
-	rc = ds_cont_child_lookup(rpt->rt_pool_uuid, entry->ie_couuid, &cont_child);
-	if (rc != 0) {
-		D_ERROR("Container "DF_UUID", ds_cont_child_lookup failed: "DF_RC"\n",
-			DP_UUID(entry->ie_couuid), DP_RC(rc));
-		vos_cont_close(coh);
-		return rc;
+		D_GOTO(close, rc);
 	}
 
 	/* Wait for EC aggregation to finish. NB: migrate needs to wait for EC aggregation to finish */
-	while (cont_child->sc_ec_agg_active) {
+	while (cont_child->sc_ec_agg_active &&
+	       rpt->rt_rebuild_op != RB_OP_RECLAIM &&
+	       rpt->rt_rebuild_op != RB_OP_FAIL_RECLAIM) {
 		D_ASSERTF(rpt->rt_pool->sp_rebuilding >= 0, DF_UUID" rebuilding %d\n",
 			  DP_UUID(rpt->rt_pool_uuid), rpt->rt_pool->sp_rebuilding);
 			/* Wait for EC aggregation to abort before discard the object */
-		D_DEBUG(DB_REBUILD, DF_UUID" wait for ec agg abort.\n",
-			DP_UUID(entry->ie_couuid));
+		D_INFO(DF_UUID" wait for ec agg abort.\n", DP_UUID(entry->ie_couuid));
 		dss_sleep(1000);
 		if (rpt->rt_abort || rpt->rt_finishing) {
 			D_DEBUG(DB_REBUILD, DF_CONT" rebuild op %s ver %u abort %u/%u.\n",
@@ -866,6 +889,7 @@ rebuild_container_scan_cb(daos_handle_t ih, vos_iter_entry_t *entry,
 	param.ip_flags = VOS_IT_FOR_MIGRATION;
 	uuid_copy(arg->co_uuid, entry->ie_couuid);
 	arg->snapshot_cnt = snapshot_cnt;
+	arg->cont_child = cont_child;
 
 	/* If there is no snapshots, then rebuild does not need to migrate
 	 * punched objects at all. Ideally, it should ignore any objects
@@ -881,8 +905,11 @@ rebuild_container_scan_cb(daos_handle_t ih, vos_iter_entry_t *entry,
 close:
 	vos_cont_close(coh);
 
-	if (cont_child != NULL)
+	if (cont_child != NULL) {
+		cont_child->sc_rebuilding = 0;
+		ABT_cond_broadcast(cont_child->sc_rebuild_cond);
 		ds_cont_child_put(cont_child);
+	}
 
 	D_DEBUG(DB_REBUILD, DF_UUID"/"DF_UUID" iterate cont done: "DF_RC"\n",
 		DP_UUID(rpt->rt_pool_uuid), DP_UUID(entry->ie_couuid),
@@ -1206,8 +1233,11 @@ rebuild_tgt_scan_handler(crt_rpc_t *rpc)
 	if (tls && tls->rebuild_pool_status == 0 && rc != 0)
 		tls->rebuild_pool_status = rc;
 
-	if (rpt)
+	if (rpt) {
+		if (rc)
+			rpt_delete(rpt);
 		rpt_put(rpt);
+	}
 	ro = crt_reply_get(rpc);
 	ro->rso_status = rc;
 	ro->rso_stable_epoch = d_hlc_get();
diff --git a/src/rebuild/srv.c b/src/rebuild/srv.c
index 90e1bf0fc22..daac6ac3912 100644
--- a/src/rebuild/srv.c
+++ b/src/rebuild/srv.c
@@ -1,5 +1,5 @@
 /**
- * (C) Copyright 2016-2023 Intel Corporation.
+ * (C) Copyright 2016-2024 Intel Corporation.
  *
  * SPDX-License-Identifier: BSD-2-Clause-Patent
  */
@@ -207,13 +207,38 @@ rebuild_get_global_dtx_resync_ver(struct rebuild_global_pool_tracker *rgt)
 	return min;
 }
 
+static void
+rpt_insert(struct rebuild_tgt_pool_tracker *rpt)
+{
+	D_ASSERT(dss_get_module_info()->dmi_xs_id == 0);
+	ABT_rwlock_wrlock(rebuild_gst.rg_ttl_rwlock);
+	d_list_add(&rpt->rt_list, &rebuild_gst.rg_tgt_tracker_list);
+	ABT_rwlock_unlock(rebuild_gst.rg_ttl_rwlock);
+}
+
+void
+rpt_delete(struct rebuild_tgt_pool_tracker *rpt)
+{
+	D_ASSERT(dss_get_module_info()->dmi_xs_id == 0);
+	ABT_rwlock_wrlock(rebuild_gst.rg_ttl_rwlock);
+	d_list_del_init(&rpt->rt_list);
+	ABT_rwlock_unlock(rebuild_gst.rg_ttl_rwlock);
+}
+
 struct rebuild_tgt_pool_tracker *
 rpt_lookup(uuid_t pool_uuid, uint32_t opc, unsigned int ver, unsigned int gen)
 {
 	struct rebuild_tgt_pool_tracker	*rpt;
 	struct rebuild_tgt_pool_tracker	*found = NULL;
+	bool				 locked = false;
 
-	/* Only stream 0 will access the list */
+	/* System XS or VOS target XS (obj_inflight_io_check() -> ds_rebuild_running_query())
+	 * possibly access the list, need to hold rdlock only for VOS XS.
+	 */
+	if (dss_get_module_info()->dmi_xs_id != 0) {
+		ABT_rwlock_rdlock(rebuild_gst.rg_ttl_rwlock);
+		locked = true;
+	}
 	d_list_for_each_entry(rpt, &rebuild_gst.rg_tgt_tracker_list, rt_list) {
 		if (uuid_compare(rpt->rt_pool_uuid, pool_uuid) == 0 &&
 		    rpt->rt_finishing == 0 &&
@@ -225,6 +250,8 @@ rpt_lookup(uuid_t pool_uuid, uint32_t opc, unsigned int ver, unsigned int gen)
 			break;
 		}
 	}
+	if (locked)
+		ABT_rwlock_unlock(rebuild_gst.rg_ttl_rwlock);
 
 	return found;
 }
@@ -1037,16 +1064,45 @@ rpt_get(struct rebuild_tgt_pool_tracker	*rpt)
 	ABT_mutex_unlock(rpt->rt_lock);
 }
 
+static int
+rpt_put_destroy(void *data)
+{
+	struct rebuild_tgt_pool_tracker	*rpt = data;
+
+	rpt_destroy(rpt);
+	return 0;
+}
+
 void
-rpt_put(struct rebuild_tgt_pool_tracker	*rpt)
+rpt_put(struct rebuild_tgt_pool_tracker *rpt)
 {
+	bool	zombie;
+	int	rc;
+
 	ABT_mutex_lock(rpt->rt_lock);
 	rpt->rt_refcount--;
 	D_ASSERT(rpt->rt_refcount >= 0);
 	D_DEBUG(DB_REBUILD, "rpt %p ref %d\n", rpt, rpt->rt_refcount);
 	if (rpt->rt_refcount == 1 && rpt->rt_finishing)
 		ABT_cond_signal(rpt->rt_fini_cond);
+	zombie = (rpt->rt_refcount == 0);
 	ABT_mutex_unlock(rpt->rt_lock);
+	if (!zombie)
+		return;
+
+	if (dss_get_module_info()->dmi_xs_id == 0) {
+		rpt_destroy(rpt);
+	} else {
+		/* Possibly triggered by VOS target XS by obj_inflight_io_check() ->
+		 * ds_rebuild_running_query(), but rpt_destroy() -> ds_pool_put() can only
+		 * be called in system XS.
+		 * If dss_ult_execute failed that due to fatal system error (no memory
+		 * or ABT failure), throw an ERR log.
+		 */
+		rc = dss_ult_execute(rpt_put_destroy, rpt, NULL, NULL, DSS_XS_SYS, 0, 0);
+		if (rc)
+			DL_ERROR(rc, "failed to destroy rpt %p", rpt);
+	}
 }
 
 static void
@@ -1706,7 +1762,6 @@ void
 ds_rebuild_abort(uuid_t pool_uuid, unsigned int ver, unsigned int gen, uint64_t term)
 {
 	struct rebuild_tgt_pool_tracker *rpt;
-	struct rebuild_tgt_pool_tracker	*tmp;
 
 	rebuild_leader_stop(pool_uuid, ver, gen, term);
 
@@ -1714,11 +1769,14 @@ ds_rebuild_abort(uuid_t pool_uuid, unsigned int ver, unsigned int gen, uint64_t
 	while(1) {
 		bool aborted = true;
 
-		d_list_for_each_entry_safe(rpt, tmp, &rebuild_gst.rg_tgt_tracker_list, rt_list) {
+		d_list_for_each_entry(rpt, &rebuild_gst.rg_tgt_tracker_list, rt_list) {
 			if (uuid_compare(rpt->rt_pool_uuid, pool_uuid) == 0 &&
 			    (ver == (unsigned int)(-1) || rpt->rt_rebuild_ver == ver) &&
 			    (gen == (unsigned int)(-1) || rpt->rt_rebuild_gen == gen) &&
 			    (term == (uint64_t)(-1) || rpt->rt_leader_term == term)) {
+				D_INFO(DF_UUID" try abort the rpt %p op %s ver %u gen %u\n",
+				       DP_UUID(rpt->rt_pool_uuid), rpt, RB_OP_STR(rpt->rt_rebuild_op),
+				       rpt->rt_rebuild_ver, rpt->rt_rebuild_gen);
 				rpt->rt_abort = 1;
 				aborted = false;
 			}
@@ -2139,16 +2197,11 @@ rebuild_tgt_fini(struct rebuild_tgt_pool_tracker *rpt)
 		       DP_UUID(rpt->rt_pool_uuid), DP_RC(rc));
 	/* destroy the migrate_tls of 0-xstream */
 	ds_migrate_stop(rpt->rt_pool, rpt->rt_rebuild_ver, rpt->rt_rebuild_gen);
-	d_list_del_init(&rpt->rt_list);
-	rpt_put(rpt);
-	/* No one should access rpt after rebuild_fini_one.
-	 */
-	D_ASSERT(rpt->rt_refcount == 0);
-
+	/* No one should access rpt after rebuild_fini_one. */
 	D_INFO("Finalized rebuild for "DF_UUID", map_ver=%u.\n",
 	       DP_UUID(rpt->rt_pool_uuid), rpt->rt_rebuild_ver);
-
-	rpt_destroy(rpt);
+	rpt_delete(rpt);
+	rpt_put(rpt);
 }
 
 void
@@ -2447,6 +2500,11 @@ rebuild_tgt_prepare(crt_rpc_t *rpc, struct rebuild_tgt_pool_tracker **p_rpt)
 
 	rpt->rt_rebuild_op = rsi->rsi_rebuild_op;
 
+	/* Let's add the rpt to the tracker list before IV fetch, which might yield,
+	 * to make sure the new coming request can find the rpt in the list.
+	 */
+	rpt_get(rpt);
+	rpt_insert(rpt);
 	rc = ds_pool_iv_srv_hdl_fetch(pool, &rpt->rt_poh_uuid,
 				      &rpt->rt_coh_uuid);
 	if (rc)
@@ -2486,14 +2544,16 @@ rebuild_tgt_prepare(crt_rpc_t *rpc, struct rebuild_tgt_pool_tracker **p_rpt)
 	rpt->rt_pool = pool; /* pin it */
 	ABT_mutex_unlock(rpt->rt_lock);
 
-	rpt_get(rpt);
-	d_list_add(&rpt->rt_list, &rebuild_gst.rg_tgt_tracker_list);
 	*p_rpt = rpt;
 out:
 	if (rc) {
-		if (rpt)
+		if (rpt) {
+			if (!d_list_empty(&rpt->rt_list)) {
+				rpt_delete(rpt);
+				rpt_put(rpt);
+			}
 			rpt_put(rpt);
-
+		}
 		ds_pool_put(pool);
 	}
 	daos_prop_fini(&prop);
@@ -2539,6 +2599,10 @@ init(void)
 	D_INIT_LIST_HEAD(&rebuild_gst.rg_queue_list);
 	D_INIT_LIST_HEAD(&rebuild_gst.rg_running_list);
 
+	rc = ABT_rwlock_create(&rebuild_gst.rg_ttl_rwlock);
+	if (rc != ABT_SUCCESS)
+		return dss_abterr2der(rc);
+
 	rc = ABT_mutex_create(&rebuild_gst.rg_lock);
 	if (rc != ABT_SUCCESS)
 		return dss_abterr2der(rc);
@@ -2556,6 +2620,7 @@ fini(void)
 		ABT_cond_free(&rebuild_gst.rg_stop_cond);
 
 	ABT_mutex_free(&rebuild_gst.rg_lock);
+	ABT_rwlock_free(&rebuild_gst.rg_ttl_rwlock);
 
 	rebuild_iv_fini();
 	return 0;
diff --git a/src/tests/suite/daos_obj_ec.c b/src/tests/suite/daos_obj_ec.c
index 2eef576d096..7fa47fc406b 100644
--- a/src/tests/suite/daos_obj_ec.c
+++ b/src/tests/suite/daos_obj_ec.c
@@ -1,5 +1,5 @@
 /**
- * (C) Copyright 2016-2023 Intel Corporation.
+ * (C) Copyright 2016-2024 Intel Corporation.
  *
  * SPDX-License-Identifier: BSD-2-Clause-Patent
  */
@@ -450,6 +450,27 @@ trigger_and_wait_ec_aggreation(test_arg_t *arg, daos_obj_id_t *oids,
 	daos_debug_set_params(arg->group, -1, DMG_KEY_FAIL_LOC, 0, 0, NULL);
 }
 
+void
+trigger_and_wait_ec_aggreation_2dkeys(test_arg_t *arg, daos_obj_id_t *oids,
+				      int oids_nr, char *dkey, char *dkey2, char *akey,
+				      daos_off_t offset, daos_size_t size)
+{
+	int i;
+
+	daos_debug_set_params(arg->group, -1, DMG_KEY_FAIL_LOC,
+			      DAOS_OBJ_EC_AGG_LEADER_DIFF | DAOS_FAIL_ALWAYS, 0, NULL);
+
+	print_message("wait for 35 seconds for EC aggregation.\n");
+	sleep(35);
+
+	for (i = 0; i < oids_nr; i++) {
+		ec_agg_check_replica_on_parity(arg, oids[i], dkey, akey, offset, size, false);
+		ec_agg_check_replica_on_parity(arg, oids[i], dkey2, akey, offset, size, false);
+	}
+
+	daos_debug_set_params(arg->group, -1, DMG_KEY_FAIL_LOC, 0, 0, NULL);
+}
+
 void
 ec_verify_parity_data(struct ioreq *req, char *dkey, char *akey,
 		      daos_off_t offset, daos_size_t size,
@@ -474,6 +495,37 @@ ec_verify_parity_data(struct ioreq *req, char *dkey, char *akey,
 	free(data);
 }
 
+void
+ec_verify_parity_data_fail2shards(struct ioreq *req, char *dkey, char *akey,
+				  daos_off_t offset, daos_size_t size,
+				  char *verify_data, daos_handle_t th,
+				  uint16_t shard1, uint16_t shard2)
+{
+	daos_recx_t	 recx;
+	char		*data;
+	uint16_t	 fail_shards[2];
+	uint64_t	 fail_val;
+
+	data = (char *)malloc(size);
+	assert_true(data != NULL);
+	memset(data, 0, size);
+
+	req->iod_type = DAOS_IOD_ARRAY;
+	recx.rx_nr = size;
+	recx.rx_idx = offset;
+
+	fail_shards[0] = shard1;
+	fail_shards[1] = shard2;
+	fail_val = daos_shard_fail_value(fail_shards, 2);
+	daos_fail_value_set(fail_val);
+	daos_fail_loc_set(DAOS_FAIL_SHARD_OPEN | DAOS_FAIL_ALWAYS);
+
+	lookup_recxs(dkey, akey, 1, th, &recx, 1, data, size, req);
+	assert_memory_equal(data, verify_data, size);
+	daos_fail_loc_set(0);
+	free(data);
+}
+
 static void
 ec_partial_update_agg(void **state)
 {
@@ -503,20 +555,34 @@ ec_partial_update_agg(void **state)
 		recx.rx_nr = EC_CELL_SIZE;
 		recx.rx_idx = i * EC_CELL_SIZE;
 		memset(data, 'a' + i, EC_CELL_SIZE);
-		insert_recxs("d_key", "a_key", 1, DAOS_TX_NONE, &recx, 1,
+		insert_recxs("d_key1", "a_key", 1, DAOS_TX_NONE, &recx, 1,
+			     data, EC_CELL_SIZE, &req);
+		insert_recxs("d_key2", "a_key", 1, DAOS_TX_NONE, &recx, 1,
 			     data, EC_CELL_SIZE, &req);
 	}
 
-	trigger_and_wait_ec_aggreation(arg, &oid, 1, "d_key", "a_key", 0,
-				       EC_CELL_SIZE * 8, DAOS_FORCE_EC_AGG);
+	trigger_and_wait_ec_aggreation_2dkeys(arg, &oid, 1, "d_key1", "d_key2", "a_key", 0,
+					      EC_CELL_SIZE * 8);
 
 	for (i = 0; i < 10; i++) {
 		daos_off_t offset = i * EC_CELL_SIZE;
 
 		memset(verify_data, 'a' + i, EC_CELL_SIZE);
-		ec_verify_parity_data(&req, "d_key", "a_key", offset,
-				      (daos_size_t)EC_CELL_SIZE, verify_data,
-				      DAOS_TX_NONE, true);
+		ec_verify_parity_data_fail2shards(&req, "d_key1", "a_key", offset,
+						  (daos_size_t)EC_CELL_SIZE, verify_data,
+						  DAOS_TX_NONE, 0, 3);
+		ec_verify_parity_data_fail2shards(&req, "d_key1", "a_key", offset,
+						  (daos_size_t)EC_CELL_SIZE, verify_data,
+						  DAOS_TX_NONE, 0, 2);
+		ec_verify_parity_data_fail2shards(&req, "d_key2", "a_key", offset,
+						  (daos_size_t)EC_CELL_SIZE, verify_data,
+						  DAOS_TX_NONE, 0, 1);
+		ec_verify_parity_data_fail2shards(&req, "d_key2", "a_key", offset,
+						  (daos_size_t)EC_CELL_SIZE, verify_data,
+						  DAOS_TX_NONE, 2, 3);
+		ec_verify_parity_data_fail2shards(&req, "d_key2", "a_key", offset,
+						  (daos_size_t)EC_CELL_SIZE, verify_data,
+						  DAOS_TX_NONE, 4, 5);
 	}
 	ioreq_fini(&req);
 	free(data);
@@ -612,7 +678,9 @@ ec_full_partial_update_agg(void **state)
 	recx.rx_idx =  0;
 	memset(data, 'a', full_update_size);
 	memcpy(verify_data, data, full_update_size);
-	insert_recxs("d_key", "a_key", 1, DAOS_TX_NONE, &recx, 1,
+	insert_recxs("d_key1", "a_key", 1, DAOS_TX_NONE, &recx, 1,
+		     data, full_update_size, &req);
+	insert_recxs("d_key2", "a_key", 1, DAOS_TX_NONE, &recx, 1,
 		     data, full_update_size, &req);
 
 	/* then partial stripe update */
@@ -627,15 +695,27 @@ ec_full_partial_update_agg(void **state)
 		memset(buffer, 'a' + i, partial_update_size);
 		memcpy(verify_buffer, buffer, partial_update_size);
 
-		insert_recxs("d_key", "a_key", 1, DAOS_TX_NONE, &recx, 1,
+		insert_recxs("d_key1", "a_key", 1, DAOS_TX_NONE, &recx, 1,
+			     buffer, partial_update_size, &req);
+		insert_recxs("d_key2", "a_key", 1, DAOS_TX_NONE, &recx, 1,
 			     buffer, partial_update_size, &req);
 	}
 
-	trigger_and_wait_ec_aggreation(arg, &oid, 1, "d_key", "a_key", 0,
-				       full_update_size, DAOS_FORCE_EC_AGG);
-
-	ec_verify_parity_data(&req, "d_key", "a_key", (daos_size_t)0,
-			      full_update_size, verify_data, DAOS_TX_NONE, true);
+	trigger_and_wait_ec_aggreation_2dkeys(arg, &oid, 1, "d_key1", "d_key2", "a_key", 0,
+					      full_update_size);
+
+	ec_verify_parity_data_fail2shards(&req, "d_key1", "a_key", (daos_size_t)0, full_update_size,
+					  verify_data, DAOS_TX_NONE, 0, 2);
+	ec_verify_parity_data_fail2shards(&req, "d_key1", "a_key", (daos_size_t)0, full_update_size,
+					  verify_data, DAOS_TX_NONE, 3, 4);
+	ec_verify_parity_data_fail2shards(&req, "d_key1", "a_key", (daos_size_t)0, full_update_size,
+					  verify_data, DAOS_TX_NONE, 4, 5);
+	ec_verify_parity_data_fail2shards(&req, "d_key2", "a_key", (daos_size_t)0, full_update_size,
+					  verify_data, DAOS_TX_NONE, 0, 3);
+	ec_verify_parity_data_fail2shards(&req, "d_key2", "a_key", (daos_size_t)0, full_update_size,
+					  verify_data, DAOS_TX_NONE, 3, 4);
+	ec_verify_parity_data_fail2shards(&req, "d_key2", "a_key", (daos_size_t)0, full_update_size,
+					  verify_data, DAOS_TX_NONE, 4, 5);
 	free(data);
 	free(verify_data);
 }