It's a bug or something. It just disappeared somewhere and won't come back.
Oi, you're on the X-Box, aren't you?
Known Bugs involving ED-E for the X-Box 360xbox360: If you tell ED-E to part ways and return to Primm, he may be removed from the game instead.
xbox360: Exiting Bloodborne Cave may glitch ED-E to be stuck in the opening of the cave. Even with the latest patch, ED-E will instead show up as a marker, but can't be found in the surroundings or in the cave.
xbox360: ED-E will get stuck in all the towers in Hoover Dam, mixing up what door to take to follow you. He usually ends up on the roof of the tower you exited. If you take the Elevator to Hoover Dam Offices he will usually appear. (After second patch)
pc ps3 xbox360: ED-E is often rendered unconscious via explosions which make him disappear. This may also happen when ED-E sustains enough damage while already unconscious(tested using Knock-Knock and Holorifle on knocked-out ED-E). Often, ED-E is dead, despite retaining the Enhanced Sensors Perk and the player won't receive a message about his death.
xbox360: Boomers artillery will kill ed-e, even on normal mode and you will not be informed of his death.
ps3 xbox360: When at Black Mountain, its possible that ED-E will disappear after The Courier is attacked by super mutants in the small pass with the bear traps and the large boulder, but only after the super mutants attack.[Confirmed]It can happen as well in the entrance of Vault 22.
Possible Fixes (unconfirmed) -This can be fixed by traveling to Vault 22 and using the elevator to travel to any floor if the quest involving Keeley has been completed. It is also confirmed that the Vault 22 elevator method also works if ED-E vanishes after you visit Lucky 38 and get the suite and the radar shows ED-E to be somewhere in Freeside.
- ED-E can also be returned to Primm if you have the Dead Money DLC and you go there.
I find it amazing how many Xbox exclusive bugs ED-E has.