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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.
the config and databases or the media, you mean?
if so, the former, but I mount the meadia with a read only docker volume just to be sure, because chances are I would never notice it