Confirming here also. On the same note, if you have a box of ammo within a box (300 round ammo box for example) and open the small ammo box it will be lost also. Steps to reproduce:

• Split existing ammo (not full ammo stack) within inventory
• Take an ammo box and 'empty ammo' into inventory
• Previous ammo will remain but be reduced to 0.

Also, attempting to load this 0 ammo stack into a gun will work, but you will not be able to fire any bullets.