--- a/project.ant/src/org/netbeans/spi/project/support/ant/SourcesHelper.java	
+++ a/project.ant/src/org/netbeans/spi/project/support/ant/SourcesHelper.java	
@@ -711,8 +711,7 @@ 
      * Register all external source or non-source roots using {@link FileOwnerQuery#markExternalOwner}.
      * <p>
      * Only roots added by {@link #addPrincipalSourceRoot} and {@link #addNonSourceRoot}
-     * are considered. They are registered if (and only if) they in fact fall
-     * outside of the project directory, and of course only if the folders really
+     * are considered. They are registered only if the folders really
      * exist on disk. Currently it is not defined when this file existence check
      * is done (e.g. when this method is first called, or periodically) or whether
      * folders which are created subsequently will be registered, so project type
@@ -761,8 +760,7 @@ 
      * Register all external source or non-source roots using {@link FileOwnerQuery#markExternalOwner}.
      * <p>
      * Only roots added by {@link #addPrincipalSourceRoot} and {@link #addNonSourceRoot}
-     * are considered. They are registered if (and only if) they in fact fall
-     * outside of the project directory, and of course only if the folders really
+     * are considered. They are registered only if the folders really
      * exist on disk. Currently it is not defined when this file existence check
      * is done (e.g. when this method is first called, or periodically) or whether
      * folders which are created subsequently will be registered, so project type
@@ -836,14 +834,10 @@ 
         // up calling APH.resolveFileObject repeatedly (for each property change)
         for (Root r : allRoots) {
             for (FileObject loc : r.getIncludeRoots(minimalSubfolders)) {
-                if (FileUtil.getRelativePath(pdir, loc) != null) {
-                    // Inside projdir already. Skip it.
-                    continue;
-                }
                 if (loc.isFolder()) {
                     try {
                         Project other = ProjectManager.getDefault().findProject(loc);
-                        if (other != null) {
+                        if (other != null && other != p) {
                             // This is a foreign project; we cannot own it. Skip it.
                             continue;
                         }
--- a/projectapi/src/org/netbeans/modules/projectapi/SimpleFileOwnerQueryImplementation.java	
+++ a/projectapi/src/org/netbeans/modules/projectapi/SimpleFileOwnerQueryImplementation.java	
@@ -142,8 +142,9 @@ 
                 }
             }
             
+            URI key = fileObject2URI(f);
             if (!externalOwners.isEmpty() && (folder || externalRootsIncludeNonFolders)) {
-                Reference<FileObject> externalOwnersReference = externalOwners.get(fileObject2URI(f));
+                Reference<FileObject> externalOwnersReference = externalOwners.get(key);
 
                 if (externalOwnersReference != null) {
                     FileObject externalOwner = externalOwnersReference.get();
@@ -166,16 +167,20 @@ 
                 }
             }
             if (!deserializedExternalOwners.isEmpty() && (folder || externalRootsIncludeNonFolders)) {
-                FileObject externalOwner = deserializedExternalOwners.get(fileObject2URI(f));
+                FileObject externalOwner = deserializedExternalOwners.get(key);
                 if (externalOwner != null && externalOwner.isValid()) {
                     try {
-                        // Note: will be null if there is no such project.
                         Project p = ProjectManager.getDefault().findProject(externalOwner);
-                        synchronized (this) {
-                            lastFoundKey = new WeakReference<FileObject>(f);
-                            lastFoundValue = new WeakReference<Project>(p);
+                        if (p == null) {
+                            // Now-deleted project, remove from list.
+                            deserializedExternalOwners.remove(key);
+                        } else {
+                            synchronized (this) {
+                                lastFoundKey = new WeakReference<FileObject>(f);
+                                lastFoundValue = new WeakReference<Project>(p);
+                            }
+                            return p;
                         }
-                        return p;
                     } catch (IOException e) {
                         // There is a project there, but we cannot load it...
                         LOG.log(Level.FINE, "Cannot load project.", e); //NOI18N