Can a Registered document be canceled with a legal notice ?

Can a duly registered document be cancelled with a legal notice? (ie. Registered agreement or deed before a registrar / sub registrar cancellable without a cancellation deed) if the counterclaim is filed immediately after getting knowledge of certain facts and within the limitations prescribed, whether such counter claim can be treated as filed beyond limitation by considering the date of execution of document instead of date of knowledge? Two registered tri party agreement is in place between builder and consumer, one for sale of land and another for construction over sold Land. Both the document are duly registered. In the sale of land agreement it's clearly mentioned that builder has received the payment for the land. second agreement is registered for construction on the said land. Dispute happens after builder ask for more money and stops construction. Builder then sends a notice to the consumer stating that this agreement is canceled for non payment. Consumer replies that he's willing to pay full amount mentioned in the agreement given builder builds a flat. The builder has filed a suit seeking permanent injunction stating that consumer agreement is cancelled and consumer has no right in the said flat. (No cancellation deed Is done) The matter is subjudice. The builder unknown to the court and the consumer then sales the flat to wife. And a sale deed is performed giving ownership of the land/flat to builder's wife. Is this sale deed valid since the matter is subjudice as per section 52 Transfer of property act-1882?