Thanks for coming back to this thread, @deblois. I appreciate you for following the steps provided by my colleague. 

It appears you've encountered a restriction when deleting the sales receipt. This happens when the Sales Receipt from the Square transaction you've added is still linked to the Deposit. I'm here to help provide further clarifications and steps in applying the Square payment to an invoice in QuickBooks Online (QBO).

You're on the right path of recording the invoice payment in QBO. Since adding a Square transaction from the App transactions page creates a Sales Receipt and Deposit record in QBO, we'll need to edit the Deposit to unlink the Sales Receipt and link it to the recorded invoice payment as the next step. You can follow this process:

1. Click on the Gear icon in the upper right corner.
2. Select Chart of accounts.
3. Find the bank account where the Square transactions are added. Then, select View register.
4. Find the corresponding deposit transaction at issue. To help in this task, click the Funnel icon and choose Deposit from the Transaction type drop-down list.
   
5. Select the transaction at issue. Then, hit Edit.
   
6. Uncheck the sales receipt linked and place a checkmark for the invoice payment.
7. Hit Save and close.
   

Then, you can now proceed with deleting the sales receipt. I've added a screenshot for a visual guide.

For future reference, let me add this article about reconciling accounts in QBO: Reconcile an account in QuickBooks Online.

We'll be here in the Community if you have further questions about applying a Square payment to an invoice in QBO. We'll do our best to assist. Take care.