In the upgrade guide it states Step 4) Remove obsolote configurations to remove the database options from seafile.conf and seahub.conf.
But doing so fails to upgrade the database because it thinks you have an SQLite database.
I believe it is because the upgrade/db_update_helper.py still uses the conf values to determine what type of database it uses.
Because of the failing check, upgrade on the database is not done and the seafile server fails to start because of a invalid SQL query.