I suggest adding a "reset button" (just the config button in Mod Menu would suffice) which would ask the user if they want to delete all files that would be overridden by YOSBR and then close the game for YOSBR to take effect again.

That would work as a quick fix if the user is seeing inconsistent behavior after a modpack upgrade.
Not sure how feasible that would be while keeping the mod simple and cross-compatible.