> 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.

If that's what you were doing, you won't get affected by this. This is about files/folders that were "hardlinked", which was difficult to do by accident. I think you had to hold Ctrl while dragging the file into another folder, or something like that. (The key to notice is that they're talking about one file being in multiple directories, not multiple files with identical contents.)