Still no luck with this from Shopify, years and hundreds of complaints later. So frustrating. The only work around that I’ve been able to come up with that doesn’t totally mess my book keeping bottom line up is to refund the order to a Gift Card. This works best with physical gift cards (although you waste one every time you have to use it for this reason).
Otherwise, for digital gift cards you’ll have to write down the entire card number issued right away and process it immediately so that the customer doesn’t decide to try and use it once it hits their email ( or change the customers email temporarily to one you control so you can have it emailed to you. Then change it back afterwards). Once the card is activated, recreate the order and use the gift card to pay for it. Any excess charges for shipping can be collected from the customer unless you decide to eat the cost and zero them out. I do not have the basic plan so I know if this is an option for that one. Also, it may be just as easy to allow the customer to use the gift card on the recreated draft order you send them. Either way, it’s a work around that leaves less headaches than some of the other solutions.
Of course, always communicate your plan with the customer letting them know what and how you’re going to do it so there’s no further confusion.