Hello there, @joneill.

Currently, we can delete and recreate the invoice to correct its line item. When recreating it, make sure to choose the correct shipping date, then link the payment with that invoice.

Here's how to link payment:

1. Open the created invoice, and select Receive Payment.
2. Under the Unused Credits section, click Apply Credits.
3. Put a checkmark on the checkbox to apply for the credits.
4. Select Done, then Save and Close.

I've added a screenshot below for your reference.

You can visit this article to know the different ways you can track customer transactions in QBDT: Get started with customer transaction workflows in QuickBooks Desktop.

If you have further concerns with invoices, don't hesitate to post them here. Stay safe!