The cheque bounce case is based ion the instrument alone.
You cannot file a cheque bounce case as the amount mentioned is not actual legally liable amount since the borrower had already paid a part amount of the total amount mentioned in the cheque.
In fact you cannot file a civil money recovery suit too based on this cheque, however you could have issued a legal demand notice without presenting this cheque to the bank for payment.
Your act of presenting the cheque for payment of the cheque mentioned amount can be considered as an act of fraud on your side because you know the fact that this is not the correct amount and that you have already been paid a part amount, therefore the next option before you was to issue a legal demand notice demanding the balance amount and not by presenting the cheque for the total amount.
Even now, without producing the cheque you can file a money recovery suit on the basis of the part repayment which will act as an evidence to recover the balance amount that is due to you from the borrower.