You have possession over the flat however, the sale deed is not yet executed. In this situation you should not hand over the possession to the builder for the redevelopment work until the builder has not executed a deed of conveyance.
Currently your builder cannot dispossess you from the property because you have been in peaceful possession. You have paid the price of the flat but unfortunately its sale deed is still pending. It was the responsibility of the builder to execute the sale deed before giving possession of the flat.
Get a deed of conveyance or declaration of your right
For the protection of your right in the property, you should take a deed of conveyance from the builder. If he refuses then you should file a civil suit under section 34 of the Specific Relief Act for declaration of your right.
You can not protect your right in the property on the basis of unregistered agreement to sale. After handing over the possession without any document you cannot regain your property.
Your builder wants to take possession and demolish the construction for redevelopment. If he allotted the flat to other persons after the completion of redevelopment work then you will have no documentary proof to establish your right. Hence, execution of a deed of conveyance becomes mandatory in this situation.