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Thank you for reaching out to the QuickBooks Community! I will be happy to help. I do recommend connecting with your accountant to make sure this would be the best practices for your business first. If you don't have an accountant, feel free to use our ProAdvisor services to be connected to one within your area. Many offer a free consultation.
Moreover, you could create a vendor credit or refund and then record the penalty fee as a line item on that transaction.
However, if that method is not the best route for you you can try voiding the payments and then record a separate transaction (like an expense, etc) to represent the penalty fee.
Please let me know if you need additional assistance. My team and I are here to assist. See you later!