kind of same thing happened with me when i was selling my corolla 2004,i got 80% payment on spot and 20% was left when original will be given.but my file was missing from home got the number plates but had a photocopy of file,so one day i went to the zarghoon motors to ask what must have been happened.They told us that if the file has misplaced then duplicate can be applied and u need to take an FIR for it then place its photocopy when applying for an duplicate file and some amount will be given dont remember the exact amount but i guess it was around 15000.
Khair the file was recovered from excise but if duplicate file is made,the car looses almost 40% of its normal market price.
i would suggest not to buy such car,as no one will buy it from u when u would be willing to sell it.