Sorry, but that's wrong.
I have no raid gear at all, just regular legendary and exotic armour.
I lose heavy ammo between missions and when I die, so that theory isn't right.
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I hope you're not using the Armamentarium, Heart of Praxic Fire, or Lucky Raspberry as your exotic armor. Those three exotics all have the "carry more special and heavy ammo" When you die with any armor that has an ammo upgrade perk you will lose a portion of your ammo upon death in PVE. Next time take off that armor and you'll see you lose no heavy ammo.
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Funnily enough, my Armamentarium doesn't give me this problem, but the others do :-P