Registration of allotment deed

I have a commercial IT office space. An allotment deed was signed (mentioning tenure- that allotment is permanent and forever) and a rent lease deed. Now for requesting possession of the said unit,I will need to pay Govt. duty and register the allotment deed. But builder is willing to issue a lease deed of 90 years and require this new document to be registered instead. Which of the two documents need to be registered. Please clarify