As you know, this happens on some of the maps, it's a very common issue. For most of the time, it worked for me to start that particular map as a new game, in a new slot, as instructed by the devs. BUT, when you get to the Bio-Ending.battle.2 map, it doesn't work. What you have to do is to start the Bio-Ending.battle.1 map as a new game, in a new slot. When you get to ending.battle.2 you will have your hands, ammo and everything. Hope this helps!