This is late, but may help others with the same question:

From the paid invoice, choose "Add Credit Note" and assign it to the same journal as your invoice was entered on (Customer Invoices?).  Now you have a credit note and owe your client the money.

Then go to your payment provider (Stripe?) an do a manual refund. In Stripe, I choose the transaction where the customer paid me and I choose "refund".  Authorize.net may be slightly different.

Finally go to the Credit Note and choose "PAID".  In my case, I always attach a supporting document to the Credit Note (a screen clipping from Stripe).

And that's it.

I am presuming that you already have a system in place to do the provider/bank - this transaction will be no different than normal.  The cash will come out of your bank and reconcile against Stripe.