diff --git a/artifactory/commands/transferconfig/transferconfig.go b/artifactory/commands/transferconfig/transferconfig.go
index 8760181c7..fcc9cbd4c 100644
--- a/artifactory/commands/transferconfig/transferconfig.go
+++ b/artifactory/commands/transferconfig/transferconfig.go
@@ -4,13 +4,13 @@ import (
 	"bytes"
 	"context"
 	"fmt"
-	"github.com/jfrog/gofrog/version"
 	"net/http"
 	"os"
 	"strings"
 	"time"
 
-	"github.com/jfrog/gofrog/datastructures"
+	"github.com/jfrog/gofrog/version"
+
 	"github.com/jfrog/jfrog-cli-core/v2/artifactory/commands/generic"
 	"github.com/jfrog/jfrog-cli-core/v2/artifactory/commands/transferconfig/configxmlutils"
 	commandsUtils "github.com/jfrog/jfrog-cli-core/v2/artifactory/commands/utils"
@@ -152,9 +152,6 @@ func (tcc *TransferConfigCommand) Run() (err error) {
 	}
 
 	tcc.LogTitle("Phase 5/5 - Import repositories to the target Artifactory")
-	if err = tcc.deleteConflictingRepositories(selectedRepos); err != nil {
-		return
-	}
 	if err = tcc.TransferRepositoriesToTarget(selectedRepos, remoteRepos); err != nil {
 		return
 	}
@@ -528,30 +525,6 @@ func (tcc *TransferConfigCommand) getWorkingDirParam() string {
 	return ""
 }
 
-func (tcc *TransferConfigCommand) deleteConflictingRepositories(selectedRepos map[utils.RepoType][]string) error {
-	log.Info("Deleting conflicting repositories in the target Artifactory server, if any exist...")
-	targetRepos, err := tcc.TargetArtifactoryManager.GetAllRepositories()
-	if err != nil {
-		return err
-	}
-	allSourceRepos := datastructures.MakeSet[string]()
-	for _, selectedReposWithType := range selectedRepos {
-		for _, selectedRepo := range selectedReposWithType {
-			allSourceRepos.Add(selectedRepo)
-		}
-	}
-
-	for _, targetRepo := range *targetRepos {
-		if allSourceRepos.Exists(targetRepo.Key) {
-			if err = tcc.TargetArtifactoryManager.DeleteRepository(targetRepo.Key); err != nil {
-				return err
-			}
-		}
-	}
-	log.Info("Done deleting conflicting repositories")
-	return nil
-}
-
 // Make sure that the source Artifactory version is sufficient.
 // Returns the source Artifactory version.
 func (tcc *TransferConfigCommand) validateMinVersion() error {
diff --git a/artifactory/commands/utils/transferconfigbase.go b/artifactory/commands/utils/transferconfigbase.go
index 133776982..00d3f6ea5 100644
--- a/artifactory/commands/utils/transferconfigbase.go
+++ b/artifactory/commands/utils/transferconfigbase.go
@@ -4,6 +4,7 @@ import (
 	"encoding/json"
 	"fmt"
 
+	"github.com/jfrog/gofrog/datastructures"
 	"github.com/jfrog/jfrog-cli-core/v2/artifactory/utils"
 	"github.com/jfrog/jfrog-cli-core/v2/utils/config"
 	"github.com/jfrog/jfrog-cli-core/v2/utils/coreutils"
@@ -76,6 +77,11 @@ func (tcb *TransferConfigBase) ValidateDifferentServers() error {
 
 // Create a map between the repository types to the list of repositories to transfer.
 func (tcb *TransferConfigBase) GetSelectedRepositories() (map[utils.RepoType][]string, error) {
+	allTargetRepos, err := tcb.getAllTargetRepositories()
+	if err != nil {
+		return nil, err
+	}
+
 	result := make(map[utils.RepoType][]string, len(utils.RepoTypes)+1)
 	sourceRepos, err := tcb.SourceArtifactoryManager.GetAllRepositories()
 	if err != nil {
@@ -87,6 +93,10 @@ func (tcb *TransferConfigBase) GetSelectedRepositories() (map[utils.RepoType][]s
 		if shouldIncludeRepo, err := includeExcludeFilter.ShouldIncludeRepository(sourceRepo.Key); err != nil {
 			return nil, err
 		} else if shouldIncludeRepo {
+			if allTargetRepos.Exists(sourceRepo.Key) {
+				log.Info("Repository '" + sourceRepo.Key + "' already exists in the target Artifactory server. Skipping.")
+				continue
+			}
 			repoType := utils.RepoTypeFromString(sourceRepo.Type)
 			result[repoType] = append(result[repoType], sourceRepo.Key)
 		}
@@ -132,6 +142,19 @@ func (tcb *TransferConfigBase) TransferRepositoriesToTarget(reposToTransfer map[
 	return tcb.transferVirtualRepositoriesToTarget(reposToTransfer[utils.Virtual])
 }
 
+// Get a set of all repositories in the target Artifactory server.
+func (tcb *TransferConfigBase) getAllTargetRepositories() (*datastructures.Set[string], error) {
+	targetRepos, err := tcb.TargetArtifactoryManager.GetAllRepositories()
+	if err != nil {
+		return nil, err
+	}
+	allTargetRepos := datastructures.MakeSet[string]()
+	for _, targetRepo := range *targetRepos {
+		allTargetRepos.Add(targetRepo.Key)
+	}
+	return allTargetRepos, nil
+}
+
 // Transfer local, federated, unknown, or virtual repositories
 // reposToTransfer - Repositories names to transfer
 // repoType - Repository type
diff --git a/artifactory/commands/utils/transferconfigbase_test.go b/artifactory/commands/utils/transferconfigbase_test.go
index 138f61200..dffa4784f 100644
--- a/artifactory/commands/utils/transferconfigbase_test.go
+++ b/artifactory/commands/utils/transferconfigbase_test.go
@@ -119,10 +119,10 @@ func TestValidateDifferentServers(t *testing.T) {
 }
 
 func TestGetSelectedRepositories(t *testing.T) {
-	testServer, serverDetails, _ := commonTests.CreateRtRestsMockServer(t, func(w http.ResponseWriter, r *http.Request) {
+	sourceTestServer, sourceServerDetails, _ := commonTests.CreateRtRestsMockServer(t, func(w http.ResponseWriter, _ *http.Request) {
 		w.WriteHeader(http.StatusOK)
 		repositories := &[]services.RepositoryDetails{
-			{Key: "generic-local", Type: "local"}, {Key: "generic-local-filter", Type: "local"},
+			{Key: "generic-local", Type: "local"}, {Key: "generic-local-filter", Type: "local"}, {Key: "generic-local-existed", Type: "local"},
 			{Key: "generic-remote", Type: "remote"}, {Key: "generic-filter-remote", Type: "remote"},
 			{Key: "generic-virtual", Type: "virtual"}, {Key: "filter-generic-virtual", Type: "virtual"},
 			{Key: "generic-federated", Type: "federated"}, {Key: "generic-federated-filter", Type: "federated"},
@@ -132,9 +132,18 @@ func TestGetSelectedRepositories(t *testing.T) {
 		_, err = w.Write(reposBytes)
 		assert.NoError(t, err)
 	})
-	defer testServer.Close()
+	defer sourceTestServer.Close()
+	targetTestServer, targetServerDetails, _ := commonTests.CreateRtRestsMockServer(t, func(w http.ResponseWriter, _ *http.Request) {
+		w.WriteHeader(http.StatusOK)
+		repositories := &[]services.RepositoryDetails{{Key: "generic-local-existed", Type: "local"}}
+		reposBytes, err := json.Marshal(repositories)
+		assert.NoError(t, err)
+		_, err = w.Write(reposBytes)
+		assert.NoError(t, err)
+	})
+	defer targetTestServer.Close()
 
-	transferConfigBase := createTransferConfigBase(t, serverDetails, serverDetails)
+	transferConfigBase := createTransferConfigBase(t, sourceServerDetails, targetServerDetails)
 	transferConfigBase.SetExcludeReposPatterns([]string{"*filter*"})
 	selectedRepos, err := transferConfigBase.GetSelectedRepositories()
 	assert.NoError(t, err)
diff --git a/xray/audit/npm/npm.go b/xray/audit/npm/npm.go
index 1590412dc..e9b6af9bf 100644
--- a/xray/audit/npm/npm.go
+++ b/xray/audit/npm/npm.go
@@ -33,11 +33,16 @@ func BuildDependencyTree(npmArgs []string) (dependencyTree []*xrayUtils.GraphNod
 	npmArgs = addIgnoreScriptsFlag(npmArgs)
 
 	// Calculate npm dependencies
-	dependenciesList, err := biutils.CalculateNpmDependenciesList(npmExecutablePath, currentDir, packageInfo.BuildInfoModuleId(), npmArgs, false, log.Logger)
+	dependenciesMap, err := biutils.CalculateDependenciesMap(npmExecutablePath, currentDir, packageInfo.BuildInfoModuleId(), npmArgs, log.Logger)
 	if err != nil {
 		log.Info("Used npm version:", npmVersion.GetVersion())
 		return
 	}
+	var dependenciesList []buildinfo.Dependency
+	for _, dependency := range dependenciesMap {
+		dependenciesList = append(dependenciesList, dependency.Dependency)
+	}
+
 	// Parse the dependencies into Xray dependency tree format
 	dependencyTree = []*xrayUtils.GraphNode{parseNpmDependenciesList(dependenciesList, packageInfo)}
 	return