That game duplication bug sounds like an error. As long as you renamed the copy (Corebound V2 or something), then it shouldn't be writing to the original.
If you look in your game's XML file (game.xml, it should be in the top level of the folder your game is in), you'll see a bunch of parameters inside the tags near the top. One of them should be "name". If you look at each of your game's files, check whether that parameter's value is the same or not.
For example, if it says name="Corebound" for the original and the copy, you need to change the value for the copy to something else, like name="Corebound 2".
Technically when you change the name of the game via the Game Settings option, it should be writing the new name to that file. If that's not happening, there's a bug.