Hello there, banj0byte.

We can record the correct payment as a regular VAT payment.

Let me guide you with these steps:

1. Click the VAT tab.
2. Go to the Payments tab.
3. Click Record payment.
4. Select the account.
5. Enter the Payment amount.
6. 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!