Was there a redevelopment agreement?

Was such agreement stamped and registered?

As the flat was allotted against grant of development rights, the allotment agreement would not attract any duty but would have to be registered for conferring proper title on you

There will be no stamp duty if the development agreement was duly stamped

Mere stamping the document does not cure your defective title. 

The document has to be registered. 

The maximum period to register the document is 8 months with penalty from date of signing 

As that period must already be over you will have to approach the builder to execute a fresh allotment agreement in your favour 

If the lease deed has been transferred to your name by a registered document, then you may not pay the stamp duty.

The stamp duty is paid at the time of registration of the property to an individual's name. 

Since the sale deed was not registered to your name, you may have to pay the applicable stamp duty and get the deed registered to your name, i.e., by regularisation mode when the government is announcing the amnesty scheme for this purpose. 

Dear sir/ma'am,

if you have the documents of the HIBA, you can use that to get the flat registered.

if you have not yet entered into a sale deed, it is advisable to do it as soon as possible and get it registered. you can also make an affidavit where you can state the delay in making the sale deed. you should get both the documents duly signed by the builder and two witnesses.

since, the time period of registration is over, you also require to make a fresh allotment deed.

Supplementary sharing agreement between landowners and builder should have been registered