The root cause is that on the video side, Plex uses filenames to identify content.
It does not have to be like that. Plex could use content to identify content via fingerprints.
Plex already uses fingerprinting for music.
A similar approach should be taken for video.
See here.
This does not help much now, but if Plex changed the mechanism, video collections would benefit in the future just like it now works for music.
