We're glad to have you back here, MJK Design Group.

I'm here to share additional information about the prompt you're seeing when doing it to your invoices or payments linked to estimates. Changing the customer name to a project will remove the linked transaction since the invoice was converted from an estimate. You'll want to delete the invoice and modify the customer named on the estimate. From there, create the sales transaction and apply the payment to link them under the same project.

Here's how to delete the invoice:

1. From the Sales menu, select Customers.
2. Click the customer’s name.
3. Under the Transaction List tab, look for the invoice and click the drop-down under the Action column, then choose Delete.
4. Hit Yes on the message prompt to delete the transaction.

Once done, open the estimate and change the customer name. Then, convert the transaction into an invoice. Follow the steps below:

1. In the Transaction List tab, double-click the estimate. 
2. Choose the Project on Customer drop-down.
3. Hit Save.
4. Click the Create invoice button next to the transaction amount.
5. On the pop-up, select the appropriate option and click Create Invoice.
6. From the invoice screen, click Save.

Then, link the payment by clicking the Receive payment button. Please refer to this article for more information: Record invoice payments in QuickBooks Online.

Let me know how these steps work. I'm always here if you need more help.