You know, on first glance I thought there were multiple required files in each primary folder, but it looks like there are only identical .bin and .cue files for each game. Since they are not being recognized as duplicates anyway, there should be no issue moving them up a directory. Thanks for the help!

Yes, I figured that it was the shortcut, but my concern is less about how to edit the files (I've already done that), and more a question of why the folder has suddenly decided not to show up.