Ive built and worked on alot of bikes, and Ive never seen that ever. VIN and engine numbers are completely different....Ontario does not record engine numbers along with VIN, unlike some countries and states in the US. So the only way would be to try and cross reference with Yamaha. I wish you luck with that!
IMO it should be like it is in Jamaica, when I ship a bike there the engine number is on file with the VIN. Even when I sent a replacement motor, I had to fill out papers stating what bike VIN the motor was going into. It would realy help in situations like this