Komet allows you to cancel a payment due to NSF. A negative transaction will be generated with the same information of the original payment so the invoice will be still pending to be paid. If you choose to do it, you will be able to charge a fee and a invoice will be generated under the denomination NSF.
If the payment which you want to apply a NSF fee has been generated through an overpayment, the open credits derived of that transaction will be cancelled. In case those credits have already been used for other transactions, the system will not allow to process the NSF fee.