How do I clear the Bill Pay report without changing books from many years ago?

Thanks for posting in the Community, @Sagely Sown.

You can review the transactions to locate the missing payments for the bills where you can find it on the Expenses and Vendors list and make a payment.

Here's how:

1. Go to the Expenses menu and then select Expenses.
2. Review the transactions there and locate the payments.
3. There you can click on the Bill and Make a payment.
4. Then Save and close.

You can use this article about What to expect when you switch from QuickBooks Desktop to QuickBooks Online. It includes there the Bills and bill payments.
 

Please feel free to leave a message if there's anything else I can assist. I'm always here to help. Have a good one!

Thanks for the guidance on this-I was able to sit down with our accountant & figure out a solution. Going forward we will need to do a better job of reconciliation

Thanks for the guidance on this