Issue bank draft for second cheque amount 

You can give the remaining amount to the seller via a separate cheque and can do an addendum to the sale deed which should be registered at SRO.

- You can pay the amount of that cheque by way of demand draft 

- Further, you should take an undertaking /receipt for the said payment after mentioning the DD number.

- However, the sale deed is legally valid even no payment made of one cheque

In lieu of second cheque, pay by Demand Draft (DD) the same amount to the seller and get it incorporated in the Rectification Deed, which has to be registered in the same Sub Registrar's Office in which the sale deed in your favour was registered.

Kindly make DD of same bank and take return in rejected cheque.

You can pay the amount towards the bounced cheque either by issuing a legally valid and honorable cheque or by a DD.

You can obtain a receipt for the sum settled subsequently by a different cheque by mentioning the serial number of the cheque

Pay the seller through banker's cheque/DD/fresh cheque/RTGS/online payment. There are so many options.

Dear client,  The validity of the cheque is from the date of the cheque and not from the date when the cheque book was issued by the bank to the account holder. A cheque leaf is not bad simply for being old. The validity starts from it's date of drawing. Present the cheque for collection

You may pay either through Internet banking or by means of a bank DD as agreeable to the seller.

Hello,  

1. It would be advisable ro make a bank transfer to the seller from the bank on which the cheque was drawn and get a receipt signed by the seller.
2. Alternately, If agreeable to the seller issue a new cheque for the like amount. 
3. There's no requirement of making any rectification in the Agreement.