I just want to note that this is very similar to this issue I have been having:
This issue closed after 45 days but not because it was solved. I ended up splurging on an upgrade to my equipment (got a SonicTransporter CDR) and for a while that worked. After some hiccups it was backing up successfully and reporting for duty alive every morning. Then I went on vacation for 2 weeks. Now I am back where I started. Whenever the system attempts an automatic backup, that next morning I either need to restore from backup or restart the Roon Server. I was going to go back to a new library (although i am sad to lose my playlists, is there a way to export them so they can be imported into a fresh database?) but then I saw this post. Please note that we are not the first to have this problem, and there are other reports buried in the Support list.
I have found in my current situation that I can manually backup the library successfully after cleaning up deleted files and after not much tine after restoration. I noticed that the manual backup creates a subdirectory called Roonbackups and puts the backup there whereas the automatic backups puts the backup directly into the specified directory. There must be other differences as well since the manual backup works while the automatic backup leaves the system claiming that my database is corrupt.
I have 2 other observations. First, the people having this problem, like me, are running a Linux system networked to a NAS on which the media resides. This does not appear to be happening on MacOS or on locally stored media. Second, there is a lot of churn going on in my system. It seems that every scan finds new files and deletes others, even though I have not made any changes to my media in many months. What should be happening is it should be seeing that nothing has changed. Instead I have hundreds or thousands of “deleted” and found files every scan. All of these files are playable as far as I can see. Guys, this is some kind of edge case software issue.