Phil from the Shopify Guru team here. Let me explain how the refund system works.
You can only refund the maximum amount of money that was paid by the customer within Shopify. So if a customer paid $50.00 and part of that was shipping the max you can refund for the order will be the $50.00 they paid you. You can't refund more money than the max amount that was paid for the order.
If your customer paid for the additional postage through your Shopify store, then you'll have the ability to refund him. Just locate the order and issue a refund. If they paid for it with a different method outside of Shopify you'll need to figure out a way to get the money back to them. I know people like to send people money with Paypal in scenarios like this!
Check out this doc on refunding in Shopify:
Hope this helps! Cheers!
Phil - email@example.com
This is so poor. I am in a similar situation where a customer has returned a faulty item and paid for the shipping. I would like to refund the item plus the additional shipping charges but I cannot because the refund amount if more than the customer originally paid. So dissapointing this is not an option. It is a commonplace occurence in retail and a feature that should be in place.
Now I have to go back to the customer very unprofessionally and ask for bank details or paypay just because shopify does not give us the ability to manage our own cases and money. Ridiculous.