I stumbled across the Dead Wind cavern and popped inside for a look. Then the fight broke out...
Deathclaws. Lots of them. Despatched a couple with Boone and E-DE, then E-DE just disappeared! He was fine up till then, got his new 'post patch' blue cannon and was kicking ass.
Killed off the rest of the claws, (including the Legendary, what a bastid he was!). Went outside, no E-DE. Went to the elevator at vault 22 to bring him back. Nothing. Tried the 'moveto' commands, nothing. He hasent gone back to Primm either.
Strange thing is, his marker still shows up on the world map at the Dead Wind, but not on the local map when I go back inside.
Anyone?!

Just found his marker has now gone as well! Aarrgh, where are you little buddy?!

Same thing happen to me. Only thing I can advise is to reload a previous save from when ED-E was still with you.

What, and have to go through meeting that Legendary again??!!
Actually, not a bad idea. I have a different tactic to try out involving a Fatman..

Not Upgraded ED-E: 1732d1
Weapons upgraded (took him to Followers): 1732D0
Armour upgraded (took him to BOS): 1732CF

If you find after moving him to your position that he doesn't follow you despite being in follow (rather than wait) mode, open the console, click on ED-E (and make sure it says ED-E at the top of the screen) then type:
disable (then hit return)
enable (hit return again and close the console)

This should reset his follower AI.

I have the exact same problem as the OP; ED-E disappearing around Nellis AFB. I lost him near the solar array there, inside the control room where the ants where. I waited several in-game days, checking both prim and the lucky 38 (He should return to one of these locations) with no luck. The patch came out and I could see him on the map, but no matter where I looked he couldn't be found. i even used the no-clip mode in case he 'fell out' of the map. I tried the console commands above, and his position locator disappeared from the map, but he didn't appear at my location. I again waited a week in-game to see if he would appear at either of his return locations with no luck. I tried talking to victor to get my companions to auto wait so i could do the quests that require you to leave ED-E, no luck. I just learned that you can go to Vault 22 and use the elevator to go to the 5th floor; a bug returns your companions to you. I'm going to try that.

TL:DR for those who have this problem and don't want to read a bunch of posts:

1: Try fast travel or entering a building, sometimes your companions show up
2: Talk to victor outside the Lucky 38: it causes your companions to auto wait
3: Try the Vault 22 elevator trick - take it to the fifth floor, companions should be back
4: Wait several in-game days - someyimes the companion will come back, go back to their origional location, or return to the Lucky 38
5: try the console command above

None of these worked for me, but they may work for you.
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