Mh, just a guess, but I think your issue has to do with the level template.
The Lady Vengeance has a copy of it in most levels so you don't have to load it when player make a quick trip back. That also means it copies all the objects from the previous stage when you advance in the main story.
So, you either have issues because there are copies of objects that cannot be patched out when you load an old save or it is a general issue with level templates. Just my guess.
