Stamp Duty paid on 'Agreement to Sale' but not Registered

I had bought a flat in Mumbai in 2009 when it was in under-construction stage. Along with the flat consideration I paid the builder for stamp duty too. So my "Agreement of Sale" has the stamp duty paid stamp along with the franking slip pasted on top of it. The stamp duty date on the agreement reflects the month Dec' 2009. When i realised the builder has not registered the agreement (my lack of knowledge, as it was my 1st flat I was buying) I pressed upon him in 2015 to get the same registered for which I had sent him an email request. To which they reverted verbally that the rules have changed and now until the CC is obtained the agreement cannot be registered (my flat is on 9th floor and the cc is available upto 4th floor. Note: the building is not illegal as checked with BMC the builder has to pay regularization charges and obtain the CC) The project is still in under - construction stage as it is stuck due to lack of funds at the builder end. I fear if this project is sold to another builder I would not have any legal standing due to non-registration of the "Agreement to Sale" in spite of paying stamp duty in 2009. a. Can i get the same registered (with builder or in his absence)? b. What will happen to the stamp duty paid by me? c. Do i have to pay additional stamp duty at the time of registration as per the now ready reckoner rate or I can get some relief as the builder did not get the same registered. d. Is there any alternate to secure my flat rights if registration is not possible?