Error during Registration of flat

Dear Sir, I had done a registered sale agreement when I booked my flat in Kolkata under DSR II,new alipore office. I was asked by the promoter and his advocate to pay the full fee+stamp duty at the time of sale agreement 8.1% and was told that would have to pay nothing later at the time of sale deed & final handover of the property. Later at the time of sale deed, it came to light that since I have paid the full stamp duty the registration system against my property is set as 'REGISTRY Complete'. I am been told this is a system(computer) error and would need to be changed from the backend. Its been an year since I have been following up but they are not able to get the required approval or workaround. Please can you help me with the following question ? 1) incase I cancel the Sale Agreement and go for a fresh one, will I lose the 8.1% that I have already paid ? 2) Is there any other work around to complete the registry given I have paid the stamp duty + registration fee, but because of the problem with the registration system the sale deed cannot be progress ? Many Thanks !!