How to clear invoices that have been paid that correspond to "Unapplied Payments"?

Good afternoon, @glcoug. 

Welcome to the Community! Let me share some insight into unapplied payments. 

Seems like you're thinking the Outstanding Transaction screen/pop-up is for invoices that are already paid off. However, everything under this section is unpaid or partially paid.

You're on the right screen to take care of these unapplied payments. All you need to do is select the invoices you need to pay off (the ones that match the amount of your unapplied payments). 

Review this guide for further details that could be helpful.

This should do the trick and give you a better understanding. Have a great day!

Good afternoon, Candice:

Thank you for your reply.  Unfortunately, I believe I did not explain myself very well and so I have attached a composite screenshot of my issue.  It is my understanding that if the invoices with the green check marks had been matched up with payments when they were posted, then they would not show up on this screen.  This is what happens now.  This situation is from a previous person who did the accounting.  As you can see (I apologize for the smallness), The last invoice of outstanding transaction hasn’t been paid and so it correctly shows up on this screen.  I would like to know how to “fix” the situation so that the invoices the 13 invoices that have been paid in 2019 can be cleared off this screen by matching them against the four “unapplied payments”.  I am hopeful that the screenshot helps matters.  Thank you for your assistance.  Gregg

Thanks for getting back to this thread, @Gregg. I've got your back to help clear invoices that have been paid.

To begin, let's check your reports or register if your were overstate with the same total of the 13 invoices. 

If yes, we can delete the payment associated to the invoice by unlinking them from your invoice transactions. I'll guide you how.

1. Open your QuickBooks Online (QBO) account.
2. Choose on Sales at the left pane, then click All Sales.
3. Find the payment from the list, then open the transaction.
4. From the Receive Payment window, select on Delete from the More button.
5. A pop-up window will appear that the transaction is linked to others. Click Yes, to confirm the action.
6. Repeat the steps for other payments.

Once done, receive the payment again. Then use the Unapplied payment to the invoices. For detailed steps, please see this article: Record invoice payments in QuickBooks Online

Additionally, I'll be sharing these links you can utilize to help manage your invoice and invoice payments in QuickBooks:

•  How to link a deposit to an invoice.
• Take and process payments in QuickBooks Online.

If you have any other questions about clearing paid invoices, let me know by adding a comment below. I'm always here to help. Keep safe!