Updated an order with new size

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Hi - I received an order that was paid for using a discount code, so it was at a reduced price. But the customer ordered the wrong size so before i fulfilled the order I went to remove the large item and replaced it with a smaller item (I removed the first item). The problem is, the discount was not applied when I added it to the order. 

I made the stupid mistake of saying the new item had been paid for (I was trying to save it in the order and needed to press add), so now the order looks like the customer paid more than twice than she actually did (looks like I owe her money when I don’t!!) and Shopify payouts has deducted the cost of the item I added from the payout. How do I fix this mess?