I have 12.1 files, but apparently I understood it incorrectly. You guys have v12.1 files inside v12 folder? I have a separate folders for both versions. I think I can change it though, let's see if that works.
The file is coded to work with a specific mod and this is indicated by the name of the mod, which is actually the name of the directory the mod is in, oddly enough.
So TBS probably started the game with "Erebus in the Balance v12" so it'll always look for that folder specifically when loading the game.
Unless Lock Modified Assets was turned on minor XML changes like that would be accepted and wouldn't break the game or anything like that, as far as I know. They just have to be in the folder that matches the save file.
In any case, it seems like a case of no harm no foul.