I know a way on how you can clear a short paid invoice in QuickBooks Online, dean-deja-int-co.
To clear a short paid invoice, you can record a deposit for the full invoice payment and add the fees in a negative amount. Here's how:
Click + New in the left panel.
Under Others, click Bank Deposits.
Select the invoice payment.
In the Add funds to this deposit field, choose the relevant account.
Enter the bank fees in a negative amount, under Amount.
Hit Save and close.
This will clear your invoice as complete. I recommend visiting this link: Account Management. These will provide links about managing your QuickBooks Online account, income, expenses, inventory, and running reports.
Let me know if there's anything else you need in QuickBooks, I'll be around to keep helping. Have a good one.