ED-E vanished on me a while ago. The Vault 22 Elevator fix didn't bring him back. This patch I thought maybe he was somewhere waiting for me, but no way-point, no fast travel re-appearance. I have his perk, so he's still alive (hardcoe Mode) but will I forever be stuck unable to do Rex's quest and never able to get ED-E back?

I just want to confirm so I know if I should continue to keep my hopes up or not.

I don't think that the way-points quite work as advertised. My companions don't appear as way-points on the world map (though Victor appears for some strange reason, he's hanging out at a makeshift Khan camp according to his way-point), only on the local map. If you think you might know where you left him, you'd be better off traveling there, and checking the local map (inside and outside whichever location if applicable). Also check Novac (his fallback point), or around the Lucky 38 floor (in case you went to visit Mr House at some point with ED-E still with you, this happened to my girlfriend once and her companions were off to the side of the elevator, no one told her they would wait but no matter what, companions can't go with you when you're talking to House).

the waypoints for companions is working just fine for me, is this a new character since the patch or is this a char you started before the patch.

Before the patch. I can see Lily on the main map if I leave her somewhere (tell her to stay) so I thought I would get the same with ED-E, but maybe the local map is a good option to try and find him. I have a couple of ideas where he may be. (I know for sure he is not at Primm or Lucky 38)