SOLVED: System updates resetting permissions?

[Venson]

This is not a normal issue. My intuition is that your media drives are mounted in an ill-advised location like /home where permissions are more at the mercy of the system. The NFO metadata might help as a workaround, but this issue should not be happening. No workaround should be necessary.

My media drives are mounted on /media/[user]/. Should I mount them elsewhere in fstab? Will I need to edit metadata again once I swap to the new mount location?

That might be part of your permission issues. Most mount drives under /mnt/NAME and then use subfolders for TV and movies like /mnt/NAME/TV. Yes after you moved your media folder you have to reconfigure your libraries and rescan you media