Server Version#: 1.20.0.3125
Player Version#: 4.34.4
I found a forum post, which makes logic to what I see.
The problem I got, is that I used handbrake to re-encode a bunch of files. While encoding plex scanned the newly created, still empty file, and failed to do anything with that. Once that file was fully encoded, plex scanned it again and added metadata. Next file started to encode, plex scanned the still empty file, and added it to the first empty scanned. And this is the story to the rest of all the files. They are all very different, but all are added as different versions to the first file.
Is there a way to make plex completely forget the files merged into one, and have it scan them all over, as if it has never seen them before?