I've been starting an energy weapons playthrough lately, and the replenishing ammo you get from the footlocker in the Brotherhood bunker would be helpful. The thing is, I'm also working for Mr. House in this save and his quest requires me to destroy the whole chapter. Now I know for sure that I'm not going to be able to get the ammo if i initiate the bunker's self-destruct, but does the ammo in the footlocker respawn even when I've killed all the BoS members one at a time?

I actually wondered this myself, so I tested it.

The answer is: No. Once I had finished killing off the BOS, the ammo crate didn't respawn. Thats really how it should be though, the free ammo crate is sort of an exploit as it is.

Nice tip: there is atleast 2 mini nukes and some ammo in the 3 bunkers that are vacant. Open the door as if you would go into the bunker, it's usually locked?! If you crouch you should be able to go around the rubble. Took me a sec but I love stocking up on mini nukes.

I thought the bunkers interior has rubble in the pathway leading downstairs after you self destruct the bunker.

Energy weapon ammo is pretty easy to find plus, the perks and workbench are your friend.

Thanks for the replies C: I guess I'm going to gather EW ammo the traditional way. Shouldn't be too hard once I proceed far enough.

You could side with Legion for a bit until you get Caesar's Favour, this gives you free stuff, this could have EW ammo aswell but I'm not 100% sure.
But really the BoS box shouldn't respawn since its their used ammo from training and they can't train when their dead