diff --git a/java/java.file.launcher/src/org/netbeans/modules/java/file/launcher/SharedRootData.java b/java/java.file.launcher/src/org/netbeans/modules/java/file/launcher/SharedRootData.java
index 9939a96e8152..3c9d9099224a 100644
--- a/java/java.file.launcher/src/org/netbeans/modules/java/file/launcher/SharedRootData.java
+++ b/java/java.file.launcher/src/org/netbeans/modules/java/file/launcher/SharedRootData.java
@@ -25,6 +25,8 @@
 import java.util.List;
 import java.util.Map;
 import java.util.TreeMap;
+import java.util.logging.Level;
+import java.util.logging.Logger;
 import java.util.stream.Collectors;
 import org.netbeans.api.annotations.common.CheckForNull;
 import org.netbeans.modules.java.file.launcher.api.SourceLauncher;
@@ -43,6 +45,8 @@
  */
 public class SharedRootData {
 
+    private static final Logger LOG = Logger.getLogger(SharedRootData.class.getName());
+
     private static final Map<FileObject, SharedRootData> root2Data = new HashMap<>();
 
     public static synchronized void ensureRootRegistered(FileObject root) {
@@ -104,11 +108,14 @@ private synchronized void setNewProperties(Map<String, String> newProperties) {
         }
         String joinedCommandLine = SourceLauncher.joinCommandLines(options.values());
         try {
-            if (!joinedCommandLine.equals(root.getAttribute(SingleSourceFileUtil.FILE_VM_OPTIONS))) {
+            if (
+                    !root.getFileSystem().isReadOnly() // Skip read-only FSes (like JarFileSystem)
+                    && !joinedCommandLine.equals(root.getAttribute(SingleSourceFileUtil.FILE_VM_OPTIONS))
+            ) {
                 root.setAttribute(SingleSourceFileUtil.FILE_VM_OPTIONS, joinedCommandLine);
             }
         } catch (IOException ex) {
-            Exceptions.printStackTrace(ex);
+            LOG.log(Level.INFO, "Failed to set " + SingleSourceFileUtil.FILE_VM_OPTIONS + " for " + root.getPath(), ex);
         }
     }
 
diff --git a/java/java.file.launcher/src/org/netbeans/modules/java/file/launcher/queries/MultiSourceRootProvider.java b/java/java.file.launcher/src/org/netbeans/modules/java/file/launcher/queries/MultiSourceRootProvider.java
index 47a8bad00c02..7f5061d3fac4 100644
--- a/java/java.file.launcher/src/org/netbeans/modules/java/file/launcher/queries/MultiSourceRootProvider.java
+++ b/java/java.file.launcher/src/org/netbeans/modules/java/file/launcher/queries/MultiSourceRootProvider.java
@@ -92,7 +92,7 @@ private ClassPath getSourcePath(FileObject file) {
         if (DISABLE_MULTI_SOURCE_ROOT) return null;
         synchronized (this) {
             //XXX: what happens if there's a Java file in user's home???
-            if (file.isData() && "text/x-java".equals(file.getMIMEType())) {
+            if (file.isValid() && file.isData() && "text/x-java".equals(file.getMIMEType())) {
                 return file2SourceCP.computeIfAbsent(file, f -> {
                     try {
                         String content = new String(file.asBytes(), FileEncodingQuery.getEncoding(file));