@Cluster I think I've found an issue where any game over a certain size, I'm guessing 15mb since Mother 3 is affected, delete their save files once you go to the UI.
Yeah I readded the retroarch mod with the added command. I guess save states do work so I'll be using that, but I'd much rather the normal file system worked so it was a more authentic experience. Beggars cant be choosers I guess.