I had TOTP die for one user on my Nextcloud. I tried to disable it, but it “didn’t exist”. I tried to enable it, but it was already enabled. It would come up when I used occ twofactorauth:state user. I ended up fixing it by (force) disabling the app and re-enabling it. It didn’t break any other user’s TOTP and it fixed problem-user’s TOTP. No idea what went wrong, but I get these random issues with Nextcloud sometimes.
The plus side to this is I’ve learnt how to use Mariadb and I’ve gotten better at debugging things.