Hi @justbreve
As @FaradayKeynes mentions, you would need to create a credit note on QuickFile (we have a guide on this). This will allow you to specify the VAT rates there - which by default matches the original invoice.
When you save the credit note, if the invoice has been paid (like it has in your case), you will be prompted to confirm what happens next - whether you want it to create a bank transaction for you, or whether it should hold the funds against the client for you. Seems you’re actually paying them back, select your bank account and it will record the transaction, which should then hopefully match your bank statements.
The alternative way to do this is to wait for it to show up on your bank statement or online banking, and use the bank tagging feature to tag it as a refund from a client. It has the same overall effect.
Hope that helps