Ammo used in the Master Ammo Chest system or the balancing system seems to disappear. I started the system with yellow ammo then tried upgrading to red. I produced 3.8k of red ammo in an hour and used 48 according to the "P" production screen. I checked most of my turrets that are in the system and they barely have any in them. (Likely no more then a hundred or two red ammo total.)