diff --git a/ant.freeform/src/org/netbeans/modules/ant/freeform/FreeformSources.java b/ant.freeform/src/org/netbeans/modules/ant/freeform/FreeformSources.java
--- a/ant.freeform/src/org/netbeans/modules/ant/freeform/FreeformSources.java
+++ b/ant.freeform/src/org/netbeans/modules/ant/freeform/FreeformSources.java
@@ -68,6 +68,7 @@
     public FreeformSources(FreeformProject project) {
         this.project = project;
         project.helper().addAntProjectListener(this);
+        initSources(); // have to register external build roots eagerly
     }
     
     private Sources delegate;
@@ -120,6 +121,11 @@
                 }
             }
         }
+        ProjectManager.mutex().postWriteRequest(new Runnable() {
+            public void run() {
+                h.registerExternalRoots(FileOwnerQuery.EXTERNAL_ALGORITHM_TRANSIENT);
+            }
+        });
         return h.createSources();
     }
     
@@ -142,7 +148,7 @@
 
     protected void projectOpened() {
         getSourceGroups(TYPE_GENERIC);
-        h.registerExternalRoots(FileOwnerQuery.EXTERNAL_ALGORITHM_TRANSIENT);
+        h.registerExternalRoots(FileOwnerQuery.EXTERNAL_ALGORITHM_CONFIRMED);
     }
 
     protected void projectClosed() {}
diff --git a/project.ant/src/org/netbeans/spi/project/support/ant/SourcesHelper.java b/project.ant/src/org/netbeans/spi/project/support/ant/SourcesHelper.java
--- a/project.ant/src/org/netbeans/spi/project/support/ant/SourcesHelper.java
+++ b/project.ant/src/org/netbeans/spi/project/support/ant/SourcesHelper.java
@@ -298,7 +298,7 @@
     private final List<Root> nonSourceRoots = new ArrayList<Root>();
     private final List<Root> ownedFiles = new ArrayList<Root>();
     private final List<TypedSourceRoot> typedSourceRoots = new ArrayList<TypedSourceRoot>();
-    private int registeredRootAlgorithm;
+    private int registeredRootAlgorithm = -1;
     private boolean minimalSubfolders;
     /**
      * If not null, external roots that we registered the last time.
@@ -567,13 +567,14 @@
      * otherwise the whole source root is registered.
      * @throws IllegalArgumentException if the algorithm is unrecognized
      * @throws IllegalStateException if this method is called more than once on a
-     *                               given <code>SourcesHelper</code> object
+     *                               given <code>SourcesHelper</code> object with the same algorithm
      * @since 1.26
      */
     public void registerExternalRoots (int algorithm, boolean minimalSubfolders) throws IllegalArgumentException, IllegalStateException {
-        if (lastRegisteredRoots != null) {
-            throw new IllegalStateException("registerExternalRoots was already called before"); // NOI18N
+        if (lastRegisteredRoots != null && algorithm == registeredRootAlgorithm) {
+            throw new IllegalStateException("registerExternalRoots was already called before using " + algorithm); // NOI18N
         }
+        lastRegisteredRoots = null;
         registeredRootAlgorithm = algorithm;
         this.minimalSubfolders = minimalSubfolders;
         remarkExternalRoots();
diff --git a/projectapi/src/org/netbeans/api/project/FileOwnerQuery.java b/projectapi/src/org/netbeans/api/project/FileOwnerQuery.java
--- a/projectapi/src/org/netbeans/api/project/FileOwnerQuery.java
+++ b/projectapi/src/org/netbeans/api/project/FileOwnerQuery.java
@@ -168,6 +168,12 @@
      * <strong>The external marking may be persisted across VM sessions, despite the name.</strong>
      */
     public static final int EXTERNAL_ALGORITHM_TRANSIENT = 0;
+
+    /**
+     * Takes precedence over {@link #EXTERNAL_ALGORITHM_TRANSIENT} in case of conflict.
+     * @since XXX
+     */
+    public static final int EXTERNAL_ALGORITHM_CONFIRMED = 1;
     
     /**
      * Mark an external folder or file as being owned by a particular project.
@@ -199,7 +205,10 @@
         switch (algorithm) {
         case EXTERNAL_ALGORITHM_TRANSIENT:
             // XXX check args
-            SimpleFileOwnerQueryImplementation.markExternalOwnerTransient(root, owner);
+            SimpleFileOwnerQueryImplementation.markExternalOwnerTransient(root, owner, false);
+            break;
+        case EXTERNAL_ALGORITHM_CONFIRMED:
+            SimpleFileOwnerQueryImplementation.markExternalOwnerTransient(root, owner, true);
             break;
         default:
             throw new IllegalArgumentException("No such algorithm: " + algorithm); // NOI18N
@@ -236,7 +245,10 @@
         switch (algorithm) {
         case EXTERNAL_ALGORITHM_TRANSIENT:
             // XXX check args
-            SimpleFileOwnerQueryImplementation.markExternalOwnerTransient(root, owner);
+            SimpleFileOwnerQueryImplementation.markExternalOwnerTransient(root, owner, false);
+            break;
+        case EXTERNAL_ALGORITHM_CONFIRMED:
+            SimpleFileOwnerQueryImplementation.markExternalOwnerTransient(root, owner, true);
             break;
         default:
             throw new IllegalArgumentException("No such algorithm: " + algorithm); // NOI18N
diff --git a/projectapi/src/org/netbeans/modules/projectapi/SimpleFileOwnerQueryImplementation.java b/projectapi/src/org/netbeans/modules/projectapi/SimpleFileOwnerQueryImplementation.java
--- a/projectapi/src/org/netbeans/modules/projectapi/SimpleFileOwnerQueryImplementation.java
+++ b/projectapi/src/org/netbeans/modules/projectapi/SimpleFileOwnerQueryImplementation.java
@@ -187,12 +187,20 @@
         }
         return null;
     }
+
+    private static class ConfirmableReference extends WeakReference<FileObject> {
+        final boolean confirmed;
+        ConfirmableReference(FileObject referent, boolean confirmed) {
+            super(referent);
+            this.confirmed = confirmed;
+        }
+    }
     
     /**
      * Map from external source roots to the owning project directories.
      */
-    private static final Map<URI,Reference<FileObject>> externalOwners =
-        Collections.synchronizedMap(new WeakHashMap<URI,Reference<FileObject>>());
+    private static final Map<URI,ConfirmableReference> externalOwners =
+        Collections.synchronizedMap(new WeakHashMap<URI,ConfirmableReference>());
     
     private static final Map<URI,FileObject> deserializedExternalOwners =
         Collections.synchronizedMap(new HashMap<URI,FileObject>());
@@ -246,16 +254,22 @@
     }
     
     /** @see FileOwnerQuery#markExternalOwner */
-    public static void markExternalOwnerTransient(FileObject root, Project owner) {
-        markExternalOwnerTransient(fileObject2URI(root), owner);
+    public static void markExternalOwnerTransient(FileObject root, Project owner, boolean confirmed) {
+        markExternalOwnerTransient(fileObject2URI(root), owner, confirmed);
     }
     
     /** @see FileOwnerQuery#markExternalOwner */
-    public static void markExternalOwnerTransient(URI root, Project owner) {
+    public static void markExternalOwnerTransient(URI root, Project owner, boolean confirmed) {
         externalRootsIncludeNonFolders |= !root.getPath().endsWith("/");
         if (owner != null) {
             FileObject fo = owner.getProjectDirectory();
-            externalOwners.put(root, new WeakReference<FileObject>(fo));
+            if (!confirmed) {
+                ConfirmableReference old = externalOwners.get(root);
+                if (old != null && old.confirmed && old.get() != null) {
+                    return;
+                }
+            }
+            externalOwners.put(root, new ConfirmableReference(fo, confirmed));
             deserializedExternalOwners.remove(root);
             synchronized (project2External) {
                 FileObject prjDir = owner.getProjectDirectory();