This clearly is not that high priority since nobody has run into this in the wild. I ran into it while writing the NodeDisposeTest.oldRootAsChildOfNewRootShouldNotDisposePeer method. Basically the setup is this:

        root = new Pane();
        rect = new Rectangle();
        root.getChildren().add(rect);
        scene = new Scene(root, 640, 480);
        stage = new Stage();
        stage.setScene(scene);
        stage.show();
        stage.requestFocus();
        Toolkit.getToolkit().firePulse();

        Pane root2 = new Pane();
        scene.setRoot(root2);
        root2.getChildren().add(root);
        Toolkit.getToolkit().firePulse();

The error is:

*** pgnodes.size() [0] != pgChildrenSize [1]
*** pgnodes.size validatePG() [0] != children.size() [1]

java.lang.AssertionError: validation of PGGroup children failed
at javafx.scene.Parent.validatePG(Parent.java:187)
at javafx.scene.Parent.impl_updatePeer(Parent.java:145)
at javafx.scene.layout.Region.impl_updatePeer(Region.java:2067)
at javafx.scene.Node.impl_syncPeer(Node.java:489)
at javafx.scene.Scene$ScenePulseListener.synchronizeSceneNodes(Scene.java:2198)
at javafx.scene.Scene$ScenePulseListener.pulse(Scene.java:2328)
at com.sun.javafx.tk.Toolkit.firePulse(Toolkit.java:329)