Un-registered agreement

My father purchased a flat in pune from builder in the year 1970 on Rs.5/- stamp paper, same is not registered. now he want to transfer that flat on my son name. we have prepared Gift Deed of the same. when we went for the registration of the same, that time Registrar asked for the Index - II of earlier agreement. when we say that, the said agreement is not registered, but now by this Gift Deed, we will pay all the stamp duty and registration fee in respect of the said flat. but they refused to get it registered and they asked us to first registered the said Agreement and then you can go for Gift Deed. we told them that, we are also not aware about the builder is live or not. but they refused to registered the Gift Deed and asked us to registered the said agreement. now my question is when we donot know about the Developer that he is live or not. then how my father can transfer and/or sold the said flat. Is there is any way for the same. we are ready to pay stamp duty of the same.