Removed Movie From Library But Still Shows in Media Manager

Hi,

I recently thought I'd have a bit of tidy up of my library and noticed that there were 3 of my movie files that had a number over the poster.



On further investigation drilling deeper into said movies with the media manager I found that next to the movie title was the word "unavailable".



I opened finder, went to my library folder and found that the file was there and it played perfectly. (I tested this by opening PMC, navigating to the movie and playing).

To try and solve it I moved the file from the library folder, updated the library, renamed the file (I had placed "Alien Prequel" in the title originally to remind me), placed it back in the library folder and once again updated the library.

This worked but at the same time didn't work at all. According to my Plex library I now have 2 copies of Prometheus one of which is available the other is not.



The available copy plays perfectly, the unavailable copy doesn't play. This proves there is only 1 copy of it in the library. The number over the poster in image 1 was obviously to show how many copies of that particular movie was in the library. The word unavailable in image 2 was there because it could only see 1 of the apparent 2 copies so showed that the second was unavailable.

That's all well and good, I now understand what those indicators are for.

However, why is Plex showing a second copy of a movie that is not in the library and how do I remove it? Any help would be appreciated.