Customer applied discount to invoice only to pay later.

I can share some tips on how to handle this transaction, SHibbs.

You can remove the applied discounts to those invoices. This way, you'll be able to link or match the payment accurately. If you've set up the discount as a credit memo, you can follow these steps in unapplying it:
 

1. Select Customers from the top menu bar.
2. Choose Customer Center, then head to the Transactions tab.
3. Double-click the appropriate invoice, then select the Apply Credits icon.
4. From the Previously Applied Credits window, clear the selection for credit.
5. Click Done in the Apply Credits window.
6. On the invoice, select Save & Close to complete the process.

If the discount is an item in the invoice, you can open the invoice and clear the discount item. Here's how:

1. Select Customers from the top menu bar.
2. Choose Customer Center, then head to the Transactions tab.
3. Double-click the appropriate invoice to open it.
4. Clear the discount item.
5. Click Save & Close, then choose Yes to confirm the changes.

I also recommend reading this guide to learn how to remove accidentally added vendor credits to a bill. Additionally, you can always check our Community articles here if you need some reference in completing your other QuickBooks tasks.

Feel comfortable to reach out to me again with any concerns or questions you may have. I'll always have your back.