QuickBooks Online has a feature that automatically applies available credits to the open invoices of the customer. Hence, the said invoice is partially paid. Before we correct the invoice and the applied credit, we'll need to turn off the feature mentioned earlier.
Click the Gear icon in the upper-right corner and select Account and Settings.
Select the Advanced tab and go to the Automation section.
Remove the checkmark in the Automatically apply credits box.
Click Save and Done.
Here's how to remove the applied credit from the invoice:
Go to Sales in the left panel and select Customers.
Locate the name you need in the Transaction List tab, then open the invoice you’re referring to.
Click the 1 payments made link below the Paid payment status.
Click the payment date and it will route you to the Receive Payment page.
Select More at the bottom of the Receive Payment page.
Click Delete and select Yes to confirm the action.
This will remove the credit from the invoice and will show as a fully opened invoice. From there, you can manually apply the credit to any invoice of the customer.
Moving forward, you'll not experience any automatic applying of credits to open invoices. Also, let me include these articles for additional reference about handling transactions in QBO: