I really wish there was a return to default controller settings so we didn't have to delete the config just to reset the controls. Can nuke the controller settings in:
C:\Users\USER\AppData\Roaming\sm64coopdx\sm64config.txt
Just remember to re-enable things like dynos packs, mods, classic chatbox controls, etc.
I mention this all because this was the first result I came across and I didn't feel comfortable manually resetting them, didn't even remember what they were to begin with.