You are an awesome, awesome person!
Now that I think about it, I actually have no idea how that'll work. It my thinking is correct (it usually isn't) it'll use the new meshes because that's what the weapons .u file has been told to use, with the new skins.
On the otherhand, the only reason Shifter uses the new HDTP models is because of a piece of code that Yuki wrote into Shifter that searched for new models and replaces them. Which is why, when you save the game, you can briefly see the old models flicker in and back to HD.