Are you keeping everything in Docker or are you switching to the native app ?
If moving to the native app, you must remember to match the UID/GID the native app uses.
Also, as part of the move,
Turn off all automatic scanning
Turn off Empty Trash
Give a read here. The procedure is fundamentally the same for any Linux-based environment. Make certain you understand the concepts and then adapt as required for your situation.
If the mount points are different (as seen by PMS) then this applies: