Peter here from Shopify Support!
When your customer selects Paypal to finalize their order there is a chance that Paypal API failed to send back the order confirmation which would cause it to show as paid in Paypal, but not in Shopify. This could happen either due to Paypal taking to long to return the information back to us, or your customer closing the Paypal window before they were redirected back to the Shopify checkout.
Nevertheless, the first thing you'll want to do is check your Paypal account to confirm the funds are there. If they are, then you should be able to find the customer in your abandon checkouts. Once you have the order information, you can create a draft order, and mark the order as paid so you can complete the fulfillment process.
If there's anything else I can help with please don't hesitate to reply back and I'll happily help out!
All the best,
Thanks for your reply. That makes sense. Is there currently anyway to proactivly find these before the customer emails or calls? Like a report of some type in Shopify that can help identify these? I've been told this is the first time this has ever happened but I want to make sure we identify the issue if/when it happens in the future, not the customer.
I understand why you'd want to be proactive about this, however, Shopify doesn't currently offer a report or a way to track whether or not a transaction failed. While these occurrences are rare, you could keep an eye on your Paypal to keep track of whether or not you're seeing a higher value in sales in comparison to your Shopify admin. The Paypal order should provide the customers' contact information which will allow you to reach out to them, as well as track down their abandoned cart should the order not fully transfer over.
Let me know if you have any other questions!
All the best,