I am currently running Version 0.9.9.10 on a dedicated Mac Mini. As part of the regular care and feeding, I occasionally will clean out any duplicate copies of movies that wind up on the server, usually as different resolution files. Plex makes it pretty easy to delete the desired duplicate with a click of the remote.
I my case, however, when I deleted one instance of a duplicate database movie listing, the media for the second database movie listing of the same name was suddently gone, too, but the second database entry remained. In an effort to solve this anomaly, I have recently discovered some duplicate database entries for a single movie.
So, for example, if I sort with the Duplicates filter in the Movies section, Plex might show me that I have 2 copies of "300: Rise of an Empire". Instead of deleting directly and just selecting one of the 1080p copies to target from the drop-down list, I opt instead to split the entry, so that I can examine the database parameters for each of the files that Plex thinks exist. And it turns out, Plex has created two database instances for the exact same movie. One file, one location, one quality, but two distinct database listings.
How do I remove one of these database listings without actually removing the file? This doesn't happen very often, thankfully.