Guns with more than maximum ammo can be reloaded, but it is a bug that a gun can get more than max ammo at all. Whenever max ammo gets decrease, current ammo should be ceiling'd. I think nanomachic might have used to recharge if it was made with less than full ammo (unless nano was lost), but I assume all the weirdness was cleared up when Game Hunter made it so mod order doesn't matter.