If your client has forgotten to enter their Coupon code at checkout, you can easily process a partial refund for the amount of the discount. To do this, simply login into the dashboard of your Payment Gateway (Stripe or PayPal) and process a refund from there.

Go to the Store Dashboard > Settings, and click the Edit button next to your Payment Gateway, in order to bring up the Go to Dashboard button. This will automatically redirect you to the dashboard for that Payment Gateway.