Just a shot in the dark but I've seen some people say something about one of the updates logging out accounts as a security measure. Assuming the recent updates didn't change auth stuff, maybe it's possible that it just needs to refresh the token? A glance at the code looks like it will keep trying to use the same JWT as long as it's still valid, and fall back to getting a new JWT using username/password. So deleting the JWT would make it get a new one. (Iirc JWTs have an embedded expiration, but the server can invalidate it so the bot code could in theory not know that the server can invalidate it)
Assuming you're getting the incorrect login error from Lemmy. Idk maybe I'm way off base with my guess.