Server Version#: 1.18.3.2156
Player Version#: 4.18.1
Been using Plex for a long time, and was working fine, famous last words… 
Yesterday, I was adding a couple new movies and TV shows, when I noticed (in Plex) the new ones had titles like “title_t00” or “title_t01” (these were ripped with MakeMKV and Handbrake. The former saves them using filenames like title_t00.mkv, but I was making sure the filenames were correct with Handbrake, so I figured Handbrake must have embedded the original name into the metadata somewhere.
Note that the cover art was matching up fine, but while browsing, one would see these incorrect titles rather than the filenames or anything more useful like Yogi Bear or Minions.
So, after a quick search, I found I had Easytag installed, which I assumed I used for such things previously, and proceeded to update title tags for the Yogi Bear and Minions movies, as well as about a dozen others that I noticed still had incorrect title metadata.
But when Plex refreshed, all of a sudden these were almost all missing, with some exceptions. I don’t recall that it updated things automatically, I may have done a refresh metadata for the movies library before seeing any changes. At any rate, Yogi Bear refreshed just fine, and now showed the updated title, but others were just gone. I did the “remove files, empty trash, clean bundles, optimize db, move files back” sort of deal, with all sorts of permutations, and nothing changes. I even tried removing tags completely, renaming the files (I use “Movie Title (Year).ext” syntax, tried removing the year), putting them in subfolders, and nothing works. In the logs, I can see
Dec 26, 2019 10:21:18.852 [0x7fb736ffd700] INFO - Library section 3 (Movies) will be updated because of a change in ‘"/home/sbishop/Videos/Movies"/Flushed Away (2006).m4v’
but the refresh/rescan does not result in any further logging regarding the missing files. The scan completes, and no new movies are found (the counter at the top remains the same).
On the flip side, I can move other movies out of the Movies folder, and Plex notes the change, and hides it from the view. Moving such movies back does result in them re-appearing in the library as expected.
The only way I’ve been able to get any change for the missing movies was to re-rip it from DVD (Minions), but I don’t have that option for all of them at the moment.
I saw something earlier (that I can’t find now) about Plex thinking things are “duplicate content”, but none of the ideas on that thread worked for me. Ideas?