This takes a bit of doing since you have to trial and error it until you're sure the correct version of ffmpeg is running when Jellyfin calls it (i.e., just installing ffmpeg6 may not be the fix you think it is). You would essentially create a bash script compatible with Ubuntu/Debian that runs the apt update/install of whatever you need with all the options (autoremove, etc.) to satisfy dependencies and swap paths if needed. The LSIO image has custom scripts built in, which makes this super easy and convenient, but it's not hard to do at all yourself, it's the concept of generating an entry point for your container. I'm not sure how other folks start/stop/remove their containers, though. If you're using docker-compose you could probably utilize a custom init script to update it automatically when you restart.
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