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I've been using jellyfin for years.
My best recommendation is DELAY UPDATES and back up before you update.
I have a history of updates breaking everything so you should be careful about them.
All software recommends backing up before an update, but for jellyfin the shit is real, you really want to back up.
Like the version or the media?
I have it on docker with two volumes, ./config and ./cache
I back up those before each update.
A bad Jellyfin update should not mess with your media folder in anyway. Though you should have backups of those aswell as a rule of thumb.
With respect to the media, you can mount the volume as read only, preventing Jellyfin from accidentally wiping your underlying content.
or just change the folder ownership to whatever user you use in the container, but don't give them write access. that's how I do it so I can still edit my media as root.