While this is a rare occurrence, it does happen from time to time if you are using a third-party payment provider that leads away from the Shopify checkout. If the customer completes the transaction but closes the window before being sent back to the Shopify checkout then it breaks the connection and can cause the order to not be created within your admin. If you have confirmed that the funds are in your account, and the order is appearing in your abandon checkouts then you'll need to recreate the order as a draft order.
1. Head to Orders/Drafts/Create Order:
2. Search the product(s) the customer ordered:
3. Add a 100% discount to the order to bring the value to $0
4. Add the customer to the order:
5. Select "Mark as Paid:"
Once marked as paid, you can then view the order in your orders section, to which, you can add an order note to clarify why the order was manually created. You can then proceed with your regular fulfillment process and have updates sent to the customer once the order has been shipped. You can learn more about creating draft orders through our help centre here.
Let me know if you run into any issues!