Hello there, banj0byte.
We can record the correct payment as a regular VAT payment.
Let me guide you with these steps:
- Click the VAT tab.
- Go to the Payments tab.
- Click Record payment.
- Select the account.
- Enter the Payment amount.
- Click Save.
Afterward, let's press F5 on the keyboard to refresh the page to make sure that the correct payment will sync on the system.
If you want a detailed look at what you owe, you can run a VAT Liability report. Here's a reference for more information: Check how much VAT you owe in QuickBooks Online.
I'm just a post-away if there's anything that I can help. Keep safe!