Hello, twilliam2.
Thank you for providing such a thorough explanation. From your outline, the downloaded transaction does not match the amount reflected in QuickBooks Desktop. This discrepancy may be attributed to the payment being only partial. Consequently, the downloaded transaction cannot be immediately applied to the QuickBooks system transaction.
To answer your question about " deleting a check removes it from QuickBooks, and it can't be undone," If you choose yes, will that actually remove the ACH transaction itself" Or will it just remove the incorrect payment to where we can apply correctly? No, it will not affect the transaction. However, if you decide to delete the linked transaction, it will also remove the ACH transaction. So, be careful when selecting which transaction to delete to avoid any unintended consequences.
I also suggest keeping this article for your reference: Accounts Payable workflows in QuickBooks Desktop. It has a detailed description of the two Accounts Payable workflows available at QBDT.
If you have any further questions or concerns, please don't hesitate to let me know. Have a great day!
