You have all business objects stored in one root business object.
All business objects ale linked from corresponding diagram elements AND Diagram object (that is root of diagram) has link to root business object.
Now create update feature for Diagram object, that checks if Diagram contains elements for all objects from linked root business object.
Graphiti should listen for changes on business object linked from Diagram (same way as it's done for normal diagram elements).
I would not artificially store lots of references to domain objects in your Graphiti editor. That 'pollutes' your editor.
For your goal you can use the EMF notifications (lots of tutorials and documentation available on the web). This will allow you to listen to all changes you need and do anything you want whenever an EMF object changes or is created.
We are doing exactly the same in our application. In our case we use CDO for storing objects and listen through CDO to changes in the domain objects. Based on that we update any open editors when needed.