So when i used "make weapons available", it stripped the weapon mods (such as elite scope) off of my other squad in addition to their laser rifles. However, only the weapons were now available and the weapon mods themselves just disappeared. They aren't on the original squad members and they aren't in the inventory where I can put them on new troops. They're just gone.
Unless i missed something?
Edit: it is reproducible. I did it just in the "squad view". Not worth the convenience of moving my weapons over with a single click if I lose all my mods permanently.