>If I upload the same file to two separate folders it's because I want two separate copies. If I change one of the copies, I don't want it to change the other copy.

That's precisely the behavior you'll get. You were allowed in the previous implementation to upload a file to one location and then put it in 2 locations, such that you would have changes in either location reflected the same way. This wasn't 'copying' a file, it was multiparenting it.