While we haven't run into this issue with our Shopify online e-com storefront, we did want a different/better type of fraud detection in place. We found the Shopify fraud detection to be less than optimal. So we implemented Riskified and are very happy with the service. It handles the transaction after it first comes out the cart. Once it determines an approve/deny then the transaction is either declined or else it's approved handed off to the payment processing gateway. There is a small percentage charge for any approved transactions, whereas declined transactions aren't charged. With 100% chargeback coverage if an approved transaction winds up being fraudulent. I'd highly recommend looking into them.
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