Hi @WiganStore,

Thanks for dropping by here in the Community. I can help you enter the transaction in QuickBooks and handle paid VAT from a sale of an item.

You can use the Refund receipt feature to record the reimbursement in the system. When adding an item, please make sure to fill the quantity, rate, amount, tax, and other fields accordingly.

Here's how:

1. Click the + New option in the upper-left corner.
2. Select Refund receipt or Give refund.
3. Press the Customer ▼ dropdown, then select the customer you want to refund.
4. Select the Refund From ▼ dropdown, and choose the bank you deposited the payment for the invoice.
5. Add all products or services the customer returned in the Product or service column.
6. Enter the necessary information.
7. Select Save and close. 

Regarding the paid portion of the VAT, I recommend contacting HMRC. One of them will be able to assist you regarding the payment and provide additional guidance.

For more information, as well as how to refund an overpayment or credit, I recommend the following article: Record a customer refund in QuickBooks Online.

Keep us posted if you need anything else regarding the setup. Have a great day.