I was not aware of that, but apparently it’s a SteamCMD bug that seems to impact other games, both on Windows and Linux.
Some people are saying that deleting the appmanifest_xxxxx.acf in the steam apps folder fixes it, but some other people are reporting that the fix did not work for them 
Guess I’ll have to poke at Valve to see if they have a solution to that.
There are multiple strategies for backups, including how many files and how many days of backup you want.
For example the backup could contain only the game.db file, but it could also contain the log file as well as the config folder (can be useful for postmortem examination of what happened between two launches of the game).
The system could also save in subfolders named based on the date and time of the backup.
That obviously brings the question of cleaning the backups, because with the auto-restart you can easily get gigs of data quite fast.
Also it’d be ideal to have this be able to run without shutting down the server (from my understanding, this would be very difficult and nearly impossible to do).
Well, that’s the same reason why you don’t want to CTRL-C on the main server window (like somebody asked earlier), when you do that, you have no guarantee that you are dealing with a fully saved/complete version of the game.db file.
I guess a shadow copy would work, but that brings a whole new world of pain.
Imo, auto-backup on shut-down is probably the safest, that would work nicely with the auto-restart feature.