Payment details in house registry

Obtain acknowledgment from seller of online payment and that cheque in lieu of it is being returned and take back the cheque.

Correction deed is option.

I donot think so that you will have any problem (unless it bounces back due to insufficient funds, or signature problem or for over writing on the cheque) if the seller has not yet encashed the 2nd cheque. He may ask for another cheque in lieu of the 2nd if it is time barred i.e. if the 2nd cheque, which you have given to him and he has not yet encashed it,  is more than 3 months old. If you give him another cheque in lieu of the 2nd cheque, please take back from him the 2nd time barred cheque which you have given to him earlier. 

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Thanks for your reply Kumar Doab. Could you please tell if such an acknowledgement should be on a legal written form such as via affidavit or any mode of communication would suffice?