My EDE disappeared when I was fighting in The Thorn . And now NPC react to it's presence but it's not there. I still get it's perc and he is not in Primm or wherever (I searched the thorn too). It would have been nice if I could at least fire him so I can take somebody else.
Since you say he's not in prim i presume you have tried zoning,
have you tried sleeping ?,
other than that try loading a save before they disapeared,
personally i hate ed-e they constantly get into fights with people even important quest npc's and when in peace mode.