With respect to the media, you can mount the volume as read only, preventing Jellyfin from accidentally wiping your underlying content.

https://www.destroyallsoftware.com/talks/wat

I just ran into this last night and discovered the solution as well. Unclear why they chose this migration behaviour!

On one hand, the Duras Sisters disprove your point. Then again, “You have manipulated the circumstances with the skill of a Romulan.” Yeeeeaaaahhh… Point taken.