Server Version#: Version 1.14.1.5488
For some reason plex has decided that all my tv shows belong in the same library with my movies. No changes have been made to the server in the last few months. It just decided to start doing this last night. The tv shows and movies are stored on completely different file systems
I’ve rolled back a few installs to see if it was a bug in the server but seems to be a issue in the database.
The first thing to check is the directories listed in each Library section.
I have myself made the mistake of listing /nas instead of /nas/movies .
The results were, needless to say, moderately amusing. 
Next, if any symlinks involved, verify them. Some folks will move the mounts but then symlink to make (they think) updating easier.
I found the problem. I was digging through plex and the library and didn’t bother to check the filesystem. There was a symbolic link in one of the movie directories that linked back to the root filesystem. This caused plex to go back to the top and reindex the while file system and treat it as one file system. Removing the link and the problem went away.
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