Try back-tracking.
I set Raul to wait once and after playing for 2 hours I finally noticed "Where the hell is Raul?".
And so I had to back-track to every location I've been at to find him. (Did not know about Vault 22 thing back then.)
Wikia had this to say on the problems tab with ED-E:
ED-E can disappear, but still be listed as your companion (you still will have enhanced sensors perk). NPCs will still make comments about ED-E, but he's not there. This is very problematic in instances like visiting Ceasar, as you must tell your companions to wait, but you can't because he's not there. This was on the 360, after ED-E was upgraded by the followers.