I've had this twice now, and its a bit annoying.
Setup is PMS on a MacBook Pro, running macOS Sierra (although the first time this happened, it was running OSX 10.11)
I have around 620 movies and 30 TV series in my Plex library, all of which are ripped from DVD and stored on a Synology NAS. So far, so good. I can access the media using the Plex Server on the Mac, and also from an iPad.
Now, twice, when I've added a new movie (by copying the ripped file to the NAS and choosing "update library"), Plex has decided instead to delete random chunks of my movies. In the latest occurrence, it decided my library only had 229 movies, and deleted the rest from the library.
Great, Plex, thanks for that. The remaining 229 can be viewed, and played, but the other 400-odd are not in the Library (although the physical files are present on the NAS).
If I restart Plex and then choose "Update Library", it - eventually - finds the "missing" files and restores them to the Library, although - of course - I lose any customisations of metadata.
This is a bit annoying, and it shouldn't do this, should it?
Any idea why? And how can I stop it randomly deleting stuff!
Edit: version is the latest 1.1.4.2757 and I'm on Plex Pass