Yes, this is a problem.
Under Library | the only option is to select or disable “All Content”. Which appears to be pulling from every defined Plex Library.
This will always create duplicates in this scenario:
Have Plex Libraries “! Movies” (which in Plex lists all movies in all Plex libraries) as well as “Movies HD”, “Movies SD” and “Movies - Use the Disc”. Yes, sometimes there might be a desire to specifically know if looking for an SD versus HD movie. And not all movies can be successfully, or even might be desired to be, copied up to the server.
Ditto for “! TV”, “TV SD” and “TV HD”.
Probably other valid scenarios, those are what quickly come to mind.
Bottom line, need ability to select/enable specific Plex Libraries. Not merely a take it or leave it against “all”.