This issue was a real hassle to fix, it required finding affected titles and then rematching them manually. Now all I have to do is re-analyze the library and Plex recreates the thumbnails if they are missing. How they go missing is still a mystery…
You may ask “didn’t you try re-analyzing before?” Well, remember I said it was a hassle to fix? Yeah because none of that worked. But, for some reason, unmatching it and then rematching it regenerates the missing thumbnails.