@TMNTturtlguy Not a problem, it should be good to the best of my testing abilities. I did not make a lot of changes as well, so its impact should be fairly self-contained. As such, I don't see how it would have affected the saving.
There's an option to have game-specific core options saved, maybe you had some of those set? I don't see why that would be the case, but it is a possibility. If you do have created a game core for some of your games, then yes, the is the case. If you don't, then saving the option will affect all the games (as all read from the default options).
Cheers! Thanks for helping narrow down the cause for this!