A bit late for an answer I know but on yuzu you might be using another mod that edit the same file and yuzu would not tell you that.Still doesnt work for me. Once you start a new game plus you should be back to level 1 for Rex correct with all of his skills reset to 1 as well?
This mod is incompatible with the gacha blade thingy, the playable pyra etc so just start your save without any mod but that one, save, then uncheck it and check your other mods.