I can share some details and guide you on how you can record a refund from HMRC into QuickBooks Online.
When you receive a refund from HMRC for a VAT payment, you have to record it in QuickBooks Online so that it can be matched with the associated bank transaction. If money enters your bank account without being matched in QuickBooks, your books will not balance at the end of the year.
To do so, you can follow the steps below:
Go to Taxes and then hit VAT.
Choose the All returns ▼ dropdown menu, then pick the specific VAT period you need.
Click on the View summary ▼ dropdown menu, then Record Refund.
Select the bank account the refund has gone into.
Make sure you've selected Refund under Payment Type.
Enter the refund date and amount in the appropriate fields.