diff --git a/nw/core/tree.py b/nw/core/tree.py
index aab0e563..7d1bef46 100644
--- a/nw/core/tree.py
+++ b/nw/core/tree.py
@@ -401,7 +401,12 @@ class NWTree():
             return False
         self._treeOrder.remove(tHandle)
         self._theLength = len(self._treeOrder)
+
+        if tHandle in self._treeRoots:
+            self._treeRoots.remove(tHandle)
+
         self._setTreeChanged(True)
+
         return True
 
     def __contains__(self, tHandle):
diff --git a/nw/gui/mainmenu.py b/nw/gui/mainmenu.py
index d7a0a833..c462c748 100644
--- a/nw/gui/mainmenu.py
+++ b/nw/gui/mainmenu.py
@@ -75,6 +75,9 @@ class GuiMainMenu(QMenuBar):
     ##
 
     def setAvailableRoot(self):
+        """Update the list of available root folders and set the ones
+        that are active.
+        """
         for itemClass in nwItemClass:
             if itemClass == nwItemClass.NO_CLASS:
                 continue
diff --git a/nw/gui/projtree.py b/nw/gui/projtree.py
index bcc81036..ab2fe52b 100644
--- a/nw/gui/projtree.py
+++ b/nw/gui/projtree.py
@@ -469,6 +469,7 @@ class GuiProjectTree(QTreeWidget):
             tIndex = self.indexOfTopLevelItem(trItemS)
             if trItemS.childCount() == 0:
                 self.takeTopLevelItem(tIndex)
+                del self.theProject.projTree[tHandle]
                 self.theParent.mainMenu.setAvailableRoot()
                 self._setTreeChanged(True)
             else: