Okey
so answering my own question:
Yes there is at least one database structure change from 0.48 to 0.49 (radio is added)
This would likely created problems later on if I just backup the pre update 0.48 database file with all my playlists and restored it into 0.49.
So what I did was:
During the update after the app is upgraded, but just before the service is restarted, backup the database file located in /var/lib/navidrome/navidrome.db
Wait until the update is completed.
Stop the navidrome service.
Edit the config file and restore the correct library location.
Restore the database from the backup you created
Start the service again.
Boom that worked. Easy see 