That’s a lot of versions - you must be doing hourly backups. My guess is that you’re running into a database performance issue due to all that history. If you’re using a newer canary version and don’t need ALL that history forever, consider using the newish --retention-policy parameter.
Do you happen to still have the original error? It’s possible Duplicati was complaining about files missing from the destination. If the missing files included dindex files then Duplicati would have to start downloading full archive files one at a time until it found the data needed to rebuild the database.
That’s a valid point, unfortunately at present I don’t think a rebuild can get interrupted then continued.