SOLVED: Jellyfin repeatedly not detecting all media and deleting cache

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I'll try to take a look at your logs, but my guess is this happens due to a race condition between Jellyfin and your NFS mounts. If the container starts before the NAS shares are mounted, the volumes you mounted in the container are essentially empty. When Jellyfin scans, it can't find the media. Even re-mounting the shares didn't fix the problem for me, I had to scrap the container, just as you've described.