I worked on recreate the bullet functionality in a personal mod, so I know how hard it can be to handle weapon prototypes... If you need help, you can ask me.
Did you change the logic with which it finds ammo types to convert? The old logic of looking for ammo with 'magazine' in the name was flawed.
Also, there are several extra types that the mod doesn't cover (personal equipment, defender bots, enemy units, etc)