I've a similar situation which I've now (hopefully) resolved thanks to EZEd's advice:
My Kids Movies (limited to GB-U parental rating)
My brother's movies (library points to a Qnap USB drive that holds a read only backup of my brothers content. Its his offsite backup effectively)
I get some duplicate films show up due to my brothers library which I then group with my content to avoid the duplicates appearing within Emby's Next up & Continue Watching sections.
I'd been having an issue with a collection where in the Kids profile they were unable to see one of the films within it.
It turns out that when I examined the collections xml file the path to that film was pointing to my brothers movie collection, which the Kid profile has no permission to access. Even if I removed the film from the collection and then added the film from my Kid library back into it it still showed the wrong path once the film was back in the collection.
To resolve I had to delete the collection, remove my brothers film from his library, recreate the collection, check the path now showed correctly as going to the film in the Kid movie library & then finally add his film back to his library. For some reason editing the xml directly & correcting the path did not work?
I'm hoping it does not now revert to the unwanted path, guess time will tell but maybe others with a similar setup will find this helpful.