I don’t think it would be possible for him to file a case of cheque dishonour against you under Section 138 of the Negotiable Instruments Act in the facts and circumstances mentioned by you.
For an offence under Section 138 to be made out, the cheque should have been issued "for the discharge, in whole or in part, of any debt or other liability", and then it should have been dishonoured. In your case, you have mentioned that you have already paid the amount due to him by NEFT, which implies that there is no debt or other liability pending against you. Therefore, it may not be possible for him to file the case under Section 138 of the said Act.
Moreover, after a cheque has been dishonoured, the payee is required to send a notice to the drawer of the cheque for making payment of the amount of the cheque. The drawer of the cheque has a time period of 15 days to make such payment from the date of receipt of such notice. Therefore, if at all any such notice is received by you, you can explain to him that there is no debt or other liability and that you have already made the payment to him by way of NEFT. And, in case you feel that the notice given by him is correct then you can still make the payment due to him, in which case the offence under Section 138 of the Negotiable Instruments Act would not be made out.
Dr. Ashok Dhamija is a New Delhi based Supreme Court Advocate and author of law books. Read more about him by clicking here. List of his Forum Replies. List of his other articles. List of his Quora Answers. List of his YouTube Videos.