I have a structure similar to this:

Stage {
    scene: Scene {
          content: VBox {
                    content: Group {
                         content: ClipView {
                                      content: VBox {
                                               content: node1 = Text { ...}
                                                     }
                                         }
                     }
          }
    }
}

When I remove node1 from its parent or change its visibility the stage is not updated immediately.
It gets correclty redrawn when another node in this stage is updated or the stage is updated because it was minimized or resized. Replacing the ClipView with a Group eliminates the problem.

Workaround:
Create a small node and immediately remove it after changing the ClipView->VBox content.
insert Rectangle {x:0, y:0, width:1, height: 1} into stage.scene.content; delete stage.scene.content[1];

Example source code of an application showing this problem is available on email request.