Thanks guns for the replies.
Would I need to give back the default weapon by type? Or if I had sold the one they were carrying, that's it? If this is the case, would I not be able to upgrade their default weapon then?
You'd need to give back the specific weapon you took from them, and even then, removing it from their inventory tends to break it so it won't shoot at all. It's not a bug, as the companion weapons don't even show up in their inventory without modding them.
I made that mistake, too. To fix it, first you need to remove the changes you made to the weapons, or the mod that did it for you. Then install this mod- http://www.newvegasnexus.com/downloads/file.php?id=37109. Give each of them a couple rounds of upgraded ammo corresponding to their weapon types, and after they burn through it, they should go back to being unlimited. I don't know how it worked, but it did.
If you aren't on a PC, it shouldn't have been possible to take the weapons in the first place. No clue how to fix it either.