Is there some way to change the thumbnail? It seems that the incorrect one is embedded in the file, so it shows up that way in the episode in Plex as well.
LucidRenegade
For MKV files:
mkvpropedit input.mkv --delete-attachment mime-type:image/jpeg --delete-attachment mime-type:image/png
For MP4 files, it depends on what track the image is on. It can be track 1 or 2.
So if you first do this:
ffmpeg -i input.mp4
You will see something like:
Stream #0:1(eng): Video: mjpeg (attached pic)
And then you can remove it with:
ffmpeg -i input.mp4 -map 0 -map -0:v:1 -c copy output.mp4
If you are not comfortable with the command-line, you can use: