You can use invisible colours to morph holes and transparencies.
 How to morph a shape with a hole
How to morph a shape with a hole
                                                            - In your Colour view, select an unused colour swatch and set its alpha (transparency) to 0.
                                                                     
                                                                
- Paint both holes on the source and destination drawings.
                                                                     
                                                                     
                                                                
- In the Timeline or Xsheet view, click on a cell in your morphing sequence.
                                                                     
                                                                
- Do one of the following:
- In the Tools toolbar, select the Morphing
tool.
- Press F3.
- In the Tool Properties view, enable the Flatten button. 
                                                                     
                                                                
A hole appears in the shape.
                                                                    