Hi @Vernon_Brown ,
We deal with this as well. The workaround we use is going to the Share link for the draft order (this is the same link sent in the invoice) and entering the gift card and then taking the rest of the payment there. You could also share this link with the customer so they can apply the gift card and then pay for the remaining with a credit card or other accepted form of payment. The important bit is that if you are logged into your website when you follow this link, it may replace their account email with your own, so make sure you are not logged into your website.
We know this has been brought up with Shopify before and are keeping our fingers and toes crossed that they add this as one of the payment options for draft orders to make this easier for those of us who run into this issue regularly.
Hope this helps you!
Lucinda