On a full cab replacement in Michigan, they will actually assign the truck a new VIN. Not sure about NY. But they know the replacement cab is from a salvage yard, that's why salvage yards exist.
Could you explain a little more on this. Does that mean they change the vin in the system to match the replacement cab? Do they make up a number and actually replace the vin badge on the cab? How does this vin match up to the manufacturer's coding?
I ask this because a few year back I did a color change on a truck and the next time I got stopped the officer checked the vin because the color didn't match the registration. It didn't cause a problem I just found it interesting at the time.