I'm guessing you are looking at two assemblies that have the same subassembly and want to copy the references used in one to the other.
I think you can't do that, but you can make a simplified rep of the subassembly and substituting that rep in higher level assembly simplified reps.
If the subassembly is X, then you can create a simplified rep in X called X-simplified, then in assembly A and assembly B you could create simplified reps that replaced X with X-simplified, rather than simply turning components on and off. So, while you can't copy the status of components that are part of X in assembly A to assembly B you can have the same simplified version of X in both assemblies. For individual parts assembled in A, there's not a way to copy the status of them to B.
It is the frustrating thing of the GUI that what is probably a simple array is not accessible more directly. I can guess there is a lot of verification behind the scenes that prevents things like excluding components that aren't part of the assembly as well as the notion that the list is actually a list of pointers to entries in multiple locations and not just a simple to copy list of names. I'll bet if someone was motivated to do so a Toolkit app could do this; maybe the functions are available in JLink or Weblink or the VB API.
