I got into a similar fix. I had two solar panels with added components and holes to fix them. I thought they were going to be identical so used just Paste because I was lazy and didn't want to duplicate the work on each. Then after a few hours work I realised they would have minor differences - one panel had additional fittings and holes which I didn't want on the other panel. This is a kludge but it helped me out:
Each panel was a separate sub-assembly with child components. Everything done to panel A was duplicated in panel B. Lets say each sub had four child components: a, b, c, d. I wanted a within A to be different to a within B. So with A activated, I copied a, and did Paste New which dropped the copy into the A sub. Then I renamed the copy of a for clarity, lets say to aa. Simultaneously of course a copy of a appeared in sub B automatically, and the renaming was also automatic. Then I hid a in the A sub, and hid aa in the B sub. Since a is not linked to aa, I was able to change the visible components to be different and ignore the hidden ones.
What happens when I try to move stuff with joints who knows? I guess all hell will break loose. But maybe I can duplicate the joints with the new components, or just join a to aa. I'll see.
Cheers
Alan