Hi there, @GIE.
You can delete the payment transaction to mark the invoice as unpaid in QuickBooks Desktop (QBDT). I'll guide you on how.
- Go to the customer's transactions list.
- Open the payment transaction.
- Delete the payment associated with the invoice.
On the other hand, you can record the bank charges as an expense or check. Before that, I recommend creating an expense account from the Chart of Accounts to track the fees accordingly.
- Go to the Banking page.
- Select Write Cheques.
- Fill in the information, then save the transaction.
You can learn more about handling your cheques from here: Create, modify, and print cheques.
Just in case you want to delete or void your transactions in batches in the future, open this article as your guide: Batch delete or void transactions in QuickBooks Desktop Accountant Edition.
If you have any other questions about your invoices and bank entries, let me know by adding a comment below. I'm always here to help. Have a good one!