Deleted payments can mixed up with our reconciliation, @PWL1. I'll explain this more.
Deleting a customer payment can result in an open invoice balance and disrupt your reconciliation process. To address this kind of concern, QuickBooks Desktop (QBDT) does permit you to recreate the deleted transaction impacting the balance of a closed fiscal year; however, this practice is generally not recommended. For a more detailed understanding of this process, refer to the following article: Close your books in QuickBooks Desktop.
With this, I strongly suggest consulting with your accountant to navigate the process effectively, as it impacts your financial records. Your accountant can provide precise guidance on the appropriate steps to rectify this matter.
Additionally, you can generate a Previous Reconciliation report in QBDT to display the details of the reconciliation you conducted, allowing you and your accountant to review and verify the adjustments made.
Revisit this thread if you still have concerns about handling deleted payments in QBDT. I'm here to assist you every step of the way.