Advance payments can be recorded as either an invoice payment or a credit note, and both are displayed as unused credits in the contact details page. Credit notes can be applied to invoices and excess invoice payments can be refunded.
To refund the excess invoice payment,
Click on the Unused Credits and you will be able to see a window with the split up of Credit Notes and Excess Invoice Payment.
Click on the Refund option present next to the Excess Invoice Payment.
Enter the amount and other relevant details and click on Save.
Now you can go to the Payments Received module to have view the receipt of the refund you have made.
and GST filing.