If your client paid via Stripe or PayPal, you'll need to issue the refund directly in Stripe or PayPal. Log-in directly to your account with Stripe or PayPal and follow the steps in their linked help docs.

If your client paid another way, you will need to issue a paper check or use another method for refund (though you probably knew that already).

Once that is done, you can add a negative dollar amount entry to offset the income from the initial invoice.

Click on "Accounting" in the left nav and then the "Payments & income" tab. Choose "other income" and enter a negative (-) dollar amount in the create payment module.

You'll be able to capture details here as well. Add it to the correct client, attach the original invoice or other statement of refund, and any descriptors you like.

If you accepted payment one way and send refund through a different payment method, it's probably best to keep separate accounting documents.