If I have a magazine in my gun, (tried with FNX & M4) and have extra magazines in a small container box and reloads. A duplicate of the magazine will load into the gun. The magazine will remain in world, even after relog, but the ammo is shared with the magazine still in the protector case.
So if I fire a shot with the newly reloaded weapon, one round will be ticked from the magazine in the container box and in the weapon.