Maybe the part of Rumple that is the dark one resides in his shadow and that somehow is what is killed with the dagger and Pan. Edit: I tried to use my phone for a comment and it was a fail! What I mean is we know that Rumple is separated from his shadow. Could the part that is the dark in the dark one have gone with it and could it replace Pan’s shadow in pan and be killed or “undone” with the dagger?
Hm, could be! Rumple did send his shadow off with the dagger so it would be cool if they were connected. And his shadow seems to be able to work on its own, just like Pan’s does. Plus we hear the shadow speak in this episode.