Progress Invoicing: Tying an invoice that was already paid back to an estimate.

Thanks for reaching out to the Community, @ABS2018.

Based on that information, they can delete the paid invoice and create a new one from the estimate. Then, use the Receive Payment option to apply the credit (from the deleted invoice) and mark this as Paid.

Here's how to delete the paid invoice:

1. In QuickBooks Online (QBO), go to the Sales menu at the left pane to get to the Customers page.
2. Click the customer's name to open the Transaction List.
3. Locate the invoice and tick the drop-down at the right under the Action column, then pick Delete.
4. Hit Yes to confirm.
5. Once done, find the estimate on the list, select Create invoice under the Action column and save it.

After that, here's how to apply the credit:

1. Go to the + New option at the top left to Receive Payment.
2. Select the customer's name in the drop-down.
3. In the Outstanding Transactions section, place a checkmark on the invoice.
4. In the Credits section, place a checkmark on the Unapplied Payment.
5. Hit Save and close. 

Once done, you can now set up progress invoicing for the second payment. You can refer to this article for the detailed steps on how: Set up and send progress invoices in QuickBooks Online.

Please leave a comment below if you have any additional questions, and I'll get back to you right away. I'm always here to help. Have a good one!

Thank you so much for your reply.  I was hoping there was a way to link the 2 without having to delete the original invoice and creating a new one from the estimate, but at least I have an answer and can assist my client.  Thanks again for your help!  :)