To refund a payment to your client, you must do it through your payment processor - Stripe, Square or PayPal. Once you've refunded a payment there, you can mark it as refunded in Sprout Studio.
Go to the Order in Sprout Studio.
On the invoice you'd like to mark as refunded, click the "Action" menu button (the three vertical dots at the end of the row).
Click the "Manage Payments" menu item.
Hover over the transaction/payment and click the "X" button to delete it.
If you need to re-add a partial payment or mark the transaction as partially refunded, click the "Pay" button.