There is no such thing as a dumb question. Ask away! 
Yeah, I’d start with a DB repair first. This would be a good starting point: Fix corrupted / malformed SQLite database (home-assistant_v2.db) (while it mentions home-assistant-v2.db, zigbee.db is also a Sqlite3 database).
You can do this in a number of ways; SSH, rsync, samba, etc. Whatever you use to get to your .yaml config files, that’s the mechanism that you would use.
You’ll want to shut down HA before fiddling with the database. You can leave it up when you copy the db to your local machine, but you’ll want to shut it down before replacing/deleting the zigbee.db file on your HA instance.
North Carolina, US 