I've actually done exactly that already and it didn't work. So I am fully with you on the 2nd theory. Somehow my computer or whatever it is is keeping a log SOMEHOW of the box that is selected when I first used the sharedBox mod (idek if i have a save file from back then that wasn't affected with it already) but at this point the mod got it, the box wins, I surrender. I will deal with it not being the last box I guess.
I truly appreciate the help, I know from the first comments that normally it should've been fixed already and I agree that the fact it didn't still makes no sense. I guess now I've learnt to never have a mon in the box I want when I use the sharedPC mod for the first time or something.
yeah i reloaded the backup save before I used the save, moved my mons out of the last box (50), sharedpc worked on box 50, saved. Reloaded my current day save file, obviously back to the same box because it's not the same save file as the backup. So there's no way to salvage this unless I want to play from that old backup save long ago lol.
Well this was a learning experience, all because I couldn't wait a few days for sharedpc mod to come out before I started playing