I've had a similar problem but it was resolved. I shall explain!
In 2002 I bought an MG Metro sport as I had nuked the engine in the mini at a track day and the Metro Sport has an MG Metro lump, just what I needed! I ranit as my car for a couple of months as the mini needed some other work first. Eventually the Metro was taken off the road and stripped. The engine stripped, tuned and dropped inthe mini, the rest of the usuable parts flogged on ebay and the vehicle declared SORN. in around August the remains of the shell was picked up and scrapped. I forgot to send the V5 back stating it had been scrapped until the new one arrived shortly before Christmas so I sent that one back with "SCRAPPED" written in big letters across it.
Just after CHristmas I recieved a letter saying the Sorn had expired and that I owed the £60 fine and some tax arrears of around £30. I wrote back explaining that the vehicle had been scrapped before the SORN had expired but I also included a cheque for the fine etc as I didn't want it being increased for late payment.
A week later I got a letter back saying that the matter would be dropped and they included my cheque so I could destroy it.
Guess I was just lucky!
Nick