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Hello,
When you copy an assembly, you have a choice to either rename or re-use all the parts. Pro E doesn't insist on renaming them, just be aware that if you re-use and then change that part, it will change everywhere it is used.
The other thing about Pro-e is that, unlike most other software, when you do a "save-as"... you are still looking at the original file. You have to close that... erase not displayed, and open the copied version. Once you've done that, assuming you chose the "new name" option... it shouldn't mess with your original version. if it still does, I'd log a call... something is wrong.
C
Pro/E file manipulation is a little different but always consistent & totally logical once you understand it.
One thing that few people seem to use but works very well for me is to use the file/rename "in session" functionality. You can open an assembly & it's drawing, rename both in session and have a new drawing & assembly without messing with anything on disk. You can change both to your hearts content & only save it after you have what you're after. You can do the same thing for parts. This technique is so much easier than doing a save as, closing & erasing then opening the copy.