Hi MMC2014,

If the invoice is still open or unpaid you can link the project to the particular invoice and customer. And save and send the invoice with the same steps in sending an invoice. If the invoice has been marked as paid, and you, later on, added the invoice to a project. The payment linked to the invoice will be removed or unlinked to the invoice. You'll have to link and add the payment back to the invoice.

Here's how to add a paid invoice to a project:

1. Click on the Sales tab.
2. Locate and select the invoice wanted to link to a project.
3. Click on Edit invoice.
4. Select the Customer drop-down and select the project.
5. Click on Save.

Reconnect the payment to the invoice:

1. Click on the Accounting tab, and click on Chart of accounts.
2. Locate and select the payment for the invoice.
3. Click on Edit, it will open the payment.
4. In the Outstanding Transactions section, select the invoice you wanted to link the payment to.
5. Click on Save and close.

The invoice should show in the projects tab and your projects report after.

You can check this link to learn more about Projects and Add existing invoices to QuickBooks Online Projects.

Feel free to post again in the Community if you have more questions!