I've searched around google and found lots of results from all over about companions gone missing/vanishing. I lost ED-E in vault 22 earlier today. Last time it was Victoria in BoS. With Veronica... She got stuck in the rubble after the bunker exploded behind me. With her: repeatedly going in and out of the bunker's entrance (roughly 10 times or so) she finally spawned out. I've tried the same with ED-E in vault 22, going in and out repeatably, using the elevator over and over... I also tried waiting 3 days, in fact: I waited for over a week's worth of game time. He shows up on the world map, right over vault 22. I've gone through each floor, he's no where.

I did discover that if I check my pip-boy on each floor I can see him still in vault 22 on each level except level 5 where he disappears from the map, he only appears in the world map, NOT local. Since losing him I cannot do any legion quests (you must leave your companion outside), nor get rex. Seems like I'm pretty much stuck with one option: quite the game, or skip all legion quests...

Does anyone here have a solution for this issue? I checked the bethesda FAQ and found a laughable "solution":

"To resolve this, load a save from before the creature or NPC fell through the ground.".