When you go into salvage and try to salvage one weapon as you have two of the same type. Salvage removes all weapons of the same type. Thus I'm left with no Grav-gun or plasma gun. As I noticed it on the first then replicated on the second.
Weapons that are "Duplicates" will disappear either when the original (other duplicate) is sold or salvaged from what I have experienced.
This effects equipped weapons also so If you have a duplication occur and equip one and sell/salvage another you will find the weapon is also removed from your loadout when you either start a mission or relog.