Edit: sorry, first I didn't get what you meant.I got a question.
Because you put the patch in atmosphere, is this the same if you have a custom themes installed? What i mean is when i update to a new version of atmophere , did i need to delete like on custom themes because otherwise it will fail to boot into atmophere?
No, game mods don't work like that.
Only what can make this mod unusable is game update different than what mod is supporting, not system update.