If partial advance is refunded, is GST payable on the amount not returned?

We had issued a pro-forma invoice and collected advance for a project. The deal is canceled and we have to return the advance amount after deducting some expenses and penalties. So we will not be refunding the whole of the amount but the partial amount. So we will refund only 70% of the advance.

Do we have to pay GST on the confiscated amount (30% of the advance)? Do we have to issue a tax invoice for that?

Please help as we are very confused in this regard.

We have paid GST on all the advance received and filed GSTR-3B but not yet filed the GSTR-1 (quarterly).