I would write a script to unload all his nade ammo and replace it with flare ammo and vise versa. I doubt that there is any other way to force this behaviour.� What happened when you order the unit to fire including the muzzle, mode and magazine type? i.e. unit fire [muzzle, mode, magazine] with the magazine as a flare?
If it was for a cutscene I would fake it.