I removed a serie (American Dad) that needs scene mapping to be shown correctly, and when I added it again, Sonarr ignores the scene mapping and uses file name mapping when listing episodes.
Scene numbering does not apply to files already in the series folder, those are assumed to follow the TVDB numbering already.
To get Sonarr to import those files using the scene numbering you’ll need to move them outside the series folder and then import them with Manual Import (on Wanted: Missing).