Meaning you have checked the On Deck option for all libraries you want to be in the global search scope?
What media are we talking about – e.g. movies or tv shows?
Have you verified the files are not simply ignored?
https://support.plex.tv/articles/201543057-why-is-some-of-my-content-not-found/
If that’s not it… can do a Plex Dance and pull some logs after returning the files and running the final scan? (Plex Dance: remove the files in question from the folder supervised by Plex, scan the library files, empty trash, clear bundles, return the files, scan the library files again)
