Can you not explain the suituation to the local Police. They wil then check the frame number to make sure its not stolen and they can then stamp on a new one for you and you then get the log book changed to match.
Won't do much for your second hand value though - bikes with history like that are not easy to shift.
When I got a new frame for my 900ss it came with no frame number whatsever. The Ducati dealer didn't have suitable number stamps so arranged for the local Honda dealer to do it for me. They did a cracking job which looked just like it was meant to be there. I would suggest you get it overstamped by someone who knows what they are doing and has proper stamps for the job. You could try your dealer for a start.