Is it fair to register a confirmation deed instead of sale deed?

We gave an ancestral property to a builder via a development agreement to develop. At that time, he registered three documents: GPA, Development Agreement with owner’s consideration, and a Sale Deed based on the GPA and Development Agreement (with stamp duty paid every time). Now, the developer wants to hand over the flats mentioned in the development agreement and Sale Deed, but he only registered a confirmation deed instead of the Sale Deed to the landowners. Is this a fair practice? He says we’ve already paid the stamp duty during the development agreement and Sale Deed. Is it acceptable to register only a confirmation deed during the handover?