Hi there, @Trueburton. I've got you covered, and I'll ensure you can re-link the payments to their appropriate invoices in your project here in QuickBooks Online (QBO).

To make sure everything is in order, you can remove the payments for those invoices. This way, you won't be confused when you re-link them to your invoices. I'll gladly input the steps below so you can proceed. To begin, here's how:

1. Access your QuickBooks Online company.
2. On the left navigational bar, go to the Projects tab.
3. Select the project, and then go to the Transactions section.
4. Double click on the invoice, and then click the Payment made hyperlink under the Payment Status in your invoice.
5. uncheck the invoice payment in the Outstanding Transaction section.
6. Once done, click Save and close.

You'll now see open invoices in your project's transaction section. Proceed to re-link the invoice payment by clicking your invoices and receiving payment. This time, ensure you're re-linking the appropriate invoice payments to the correct invoice. You can take note of the invoice number and the amount to avoid confusion when receiving the payment.

To start linking the payments, here's how:

1. Access your QuickBooks Online company.
2. On the left navigational bar, go to the Projects tab.
3. In the Transactions section, open the invoice one at a time.
4. Click Receive payment, and then check the box beside the appropriate invoice payment. A reminder, see the invoice number and amount to ensure it's correct.
5. Repeat the steps on your second invoice.
6. Once done, click Save and close.

In addition, I've got you this article to help you track the profitability and cost of the project: Track hourly labor costs and profitability by project in QuickBooks Online.

You can also check this page in case you'd like to add existing invoices to your project in QBO: Add existing invoices to QuickBooks Online Projects.

It's been a pleasure to have you in the Community today, @Trueburton. In case you have any additional QuickBooks-related concerns. Don't hesitate to get back to me by clicking the REPLY button. Take care, and enjoy the rest of the week!