You just made yourself a problem. There is a possibility that the car may have a junk title, could be stolen or simply someone short cut getting a title. The problem is that changing the VIN is illegal period. The car with all the money and hard work in to may leave on the back of a tow truck.
I doubt it'll come to that. But it is what it is. Like I said above, I have the title matching the dash Vin Plus a Notarized Title search on the other Vin which goes cold over 11 years ago.