While GrowthZone cannot dictate how your organization handles the accounting flow of checks/payments being returned due to NSF, we can provide an example of how our team handles this situation.
When our controller receives a returned check from the bank, they reach out to the customer/member and lets them know. They then add a note to the contact record's Billing tab, using the Billing Note section, detailing the check or payment number, amount, and date the check/payment was returned.
They then create a new invoice for the returned amount, noting in the description that it was for a returned check/payment. (You may add a charge to the new invoice to recoup any fees charged by the bank.)
While we realize this method may not work for everyone, hopefully this example will help you create a process that works for your organization's bookkeeping/accounting. Be sure to involve your accountant, as ultimately they are the ones balancing the books and they may have input or requirements that our example may not include.