Stamp Duty and Registration of Old Flat Transfer Agreement from the first Owner

My Late Father won a court battle in 1986 against the landlord of our chawl and Landlord gave a brand new flat to us against the rental room we were a tenant in. He first purchased a flat on his own name, and then transferred the ownership via the agreement of transfer without any monetary transaction. We left the tenancy rights of the rental room in return. Since 1986, Stamp Duty was not paid on the agreement. We just availed the "Stamp Duty Amnesty Scheme 2019" to pay the deficit stamp Duty. Since Stamp Duty was not paid, Agreement of Transfer of Ownership was also not Registered. As our Co-Op Hsg. Society is pushing for Conveyance Deed, we approached Sub Registrar with our Agreement having Stamp Duty paid under Amnesty Scheme. But since our Agreement is not registered, Sub Registrar refused to accept it for the Conveyance Deed. He said something which was unclear to me, which I guess he mentioned to pay stamp duty at market rates. I am not sure. As I just come to know I can no longer Register the Transfer of Ownership Agreement executed in 1986, as its been more than 8 months since the Agreement was executed. Now I have following issues, 1. What Can I do, if the first owner (i.e. Landloard) is not traceable/deceased (its been 33 years already)? 2. How to register this Agreement Dt. 1986? If Heir of my Late Father (my mom) and the Landloard (or his Heir) execute a Deed of Confirmation, do I have to pay the stamp duty all over again at the current market rate to register the Agreement even when the deficit stamp duty is already paid on the old Agreement just now under Amnesty Scheme 2019?