If you still have access to ACP, go to Configuration > Site Details and update the Board URL to the .onion address, then go to Configuration > General Configuration and update the Cookie Domain to the .onion address. After saving, go to Tools & Maintenance > Cache Manager and rebuild the settings cache.

If people are having trouble signing in to GU: logins worked at first because the browser still had valid session cookies from before the move to Tor, but once those cookies expired, new ones can't be set because the cookie domain doesn't match the .onion address. The admin needs to update cookiedomain and bburl to the .onion URL and rebuild the settings cache. However, the admin likely can't access ACP either so he'd need to fix via the database by updating the value column in the mybb_settings table where name is cookiedomain and bburl, then deleting the row in mybb_datacache where title is settings so MyBB regenerates the cache on next page load.