[XODIDOX]

Ok, but is there a way to work around the Yes/no popup and make it just run?

@marantz please report problem in the dedicated thread 337992 (thread). @Karellen can you help moving these to that thread? Thanks!

You can change the behavior with these settings:

Settings->Media->Library->Ignore different video versions on scan
This setting will set scanner action for different video versions. When enabled, Kodi will keep current behavior. Otherwise, the scanner will prompt for converting different video versions into additional versions of the original movie.

Settings->Media->Library->Ignore video extras on scan
This setting will set scanner action for video extras in "extras" folder. When enabled, Kodi will keep current behavior. Otherwise, the scanner will add video extras to library for associated movie.

Settings->Player->Videos->Play default video version
This setting will set player action for multiple movie versions. When enabled, Kodi will play the default video version without prompt. Otherwise, for movies with more than one version, Kodi will display a dialog to select the preferred video version."