Using two heavy weapon guns, whenever i complete a mission the split ammo in each weapon combines into one ammo and i have to split it again to load it into the second gun.

Does the combine happen right after a mission or after using Modify Granvir? If I had to guess, its an issue with the part replacement system putting the ammo back into the depot instead of the guns and then the autoloading system that loads any depot ammos into your guns when you finish modifying is not spreading it out. I'll look into a fix.