I haven't used XDE and it's even been a while since
Rose ...
I think you're saying the tool is copying the underlying model - classes and relationships - as well as the diagram. That's actually a pretty neat feature. We have used it to merge object models. I'm surprised it doesn't complain about matching classes, something like "do you really want to replace this class?"
If the diagram is too complicated to just replicate by hand, you might try unhooking the objects from any classes before you copy. Can you clear the object type for a column without destroying the rest of the diagram? I suppose you'd have to map them all back up in the target model and re-map the methods and all, though. Doesn't sound like much of a gain, does it.