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[TheDreadPirate]

I don't use NFOs, but from what others have said it appears there was a significant change in how Jellyfin organizes and uses NFOs in 10.9.

I'm not sure what the cleanest course of action is, but you could create a small test library and figure out how Jellyfin creates, organizes, and uses NFOs when it creates them vs an external app.

Once you have that figured out, some creative uses of the find command and loops could automate elimination or reorganization of your NFOs.