As far as i know Honda is the only manufacturer that will do this. If you buy a new frame through a Honda dealer then you can have the factory stamp the new one for you. Its a program Honda does through their dealers. You'll need to provide proof of ownership and the neck of the frame with a good vin plate will need to be turned in. Most dealers won't like to have to ship a complete frame so you may be asked to cut the neck off. Should be done anyway if there is going to be another frame out there with potentially the same vin stamp.
The neck with good vin plate, proof of ownership paperwork, and some legalese paperwork for Honda gets shipped off to Japan and 3-4 weeks later you should receive a call from the dealer to come and pick up your new frame. The good thing about doing it this way is you get to pick which year frame to buy. If you wanted the rare 04 frame then you can have that with your vin on it. May be the only one in the country to have a set up like that.