--- a/parsing.api/src/org/netbeans/modules/parsing/impl/indexing/RepositoryUpdater.java	
+++ a/parsing.api/src/org/netbeans/modules/parsing/impl/indexing/RepositoryUpdater.java	
@@ -101,6 +101,7 @@ 
 import org.netbeans.modules.parsing.api.UserTask;
 import org.netbeans.modules.parsing.impl.SourceAccessor;
 import org.netbeans.modules.parsing.impl.SourceFlags;
+import org.netbeans.modules.parsing.impl.TaskProcessor;
 import org.netbeans.modules.parsing.impl.Utilities;
 import org.netbeans.modules.parsing.impl.event.EventSupport;
 import org.netbeans.modules.parsing.impl.indexing.IndexerCache.IndexerInfo;
@@ -3863,14 +3864,14 @@ 
         private FileChangeListener binariesListener = null;
         private final Map<URL, File> sourceRoots = new HashMap<URL, File>();
         private final Map<URL, Pair<File, Boolean>> binaryRoots = new HashMap<URL, Pair<File, Boolean>>();
-        
+
         public RootsListeners() {
         }
 
         public void setListener(FileChangeListener sourcesListener, FileChangeListener binariesListener) {
             assert (sourcesListener != null && binariesListener != null) || (sourcesListener == null && binariesListener == null) :
                 "Both sourcesListener and binariesListener must either be null or non-null"; //NOI18N
-            
+            //todo: remove removeRecursiveListener from synchronized block
             synchronized (this) {
                 if (sourcesListener != null) {
                     assert this.sourcesListener == null : "Already using " + this.sourcesListener + "and " + this.binariesListener //NOI18N
@@ -3923,13 +3924,14 @@ 
         }
 
         private void interruptibleAddRecursiveListener(URL root, boolean sourceRoot) {
+            Pair<File,FileChangeListener> toAdd = null;
             synchronized (this) {
                 if (sourceRoot) {
                     if (sourcesListener != null) {
                         if (!sourceRoots.containsKey(root) && root.getProtocol().equals("file")) { //NOI18N
                             try {
                                 File f = new File(root.toURI());
-                                FileUtil.addRecursiveListener(sourcesListener, f);
+                                toAdd = Pair.of (f,sourcesListener);
                                 sourceRoots.put(root, f);
                             } catch (URISyntaxException use) {
                                 LOGGER.log(Level.INFO, null, use);
@@ -3953,7 +3955,7 @@ 
                                     FileUtil.addFileChangeListener(binariesListener, f);
                                 } else {
                                     // listening on a folder
-                                    FileUtil.addRecursiveListener(binariesListener, f);
+                                    toAdd = Pair.of(f,binariesListener);
                                 }
                                 binaryRoots.put(root, Pair.of(f, archiveUrl != null));
                             }
@@ -3961,30 +3963,38 @@ 
                     }
                 }
             }
-        }
-
-        public void remove(URL root, boolean sourceRoot) {
-            synchronized (this) {
-                if (sourceRoot) {
-                    if (sourcesListener != null) {
-                        File f = sourceRoots.remove(root);
-                        if (f != null) {
-                            safeRemoveRecursiveListener(sourcesListener, f);
-                        }
-                    }
-                } else {
-                    if (binariesListener != null) {
-                        Pair<File, Boolean> pair = binaryRoots.remove(root);
-                        if (pair != null) {
-                            if (pair.second) {
-                                FileUtil.removeFileChangeListener(binariesListener, pair.first);
-                            } else {
-                                safeRemoveRecursiveListener(binariesListener, pair.first);
-                            }
-                        }
-                    }
-                }
-            }
+            if (toAdd != null) {
+                FileUtil.addRecursiveListener(toAdd.second, toAdd.first);
+            }
+        }
+
+        public void remove(final URL root, final boolean sourceRoot) {
+            final RequestProcessor.Task task = RP.post(new Runnable() {     //Serialize requests into single thread
+                public @Override void run() {
+                    synchronized (this) {   //Synchronized to ensure visibility
+                        if (sourceRoot) {
+                            if (sourcesListener != null) {
+                                File f = sourceRoots.remove(root);
+                                if (f != null) {
+                                    safeRemoveRecursiveListener(sourcesListener, f);
+                                }
+                            }
+                        } else {
+                            if (binariesListener != null) {
+                                Pair<File, Boolean> pair = binaryRoots.remove(root);
+                                if (pair != null) {
+                                    if (pair.second) {
+                                        FileUtil.removeFileChangeListener(binariesListener, pair.first);
+                                    } else {
+                                        safeRemoveRecursiveListener(binariesListener, pair.first);
+                                    }
+                                }
+                            }
+                        }
+                    }
+                }
+            });
+            task.waitFinished();
         }
 
         private void safeRemoveRecursiveListener(FileChangeListener listener, File path) {