I have numerous movies and TV seasons that have been added to plex server, but, do not show in the listings. I have deleted the files, scanned library and a week later added back (sometime from a different drive) and they still do not show up. In some cases, I see the image show, then disappears.
In Plex Web, filter the view to search for duplicates (view the desired library, click on “All” and choose “Duplicates.”). Make sure Plex has not inadvertently matched the new media to an existing movie/show. Filtering for Unmatched may provide useful information as well.
Perform the Plex Dance when moving/re-naming/deleting/etc media. This clears out any incorrect information from the Plex database.