If you have eBay or Amazon marketplace connected to your Shopify, and see those orders created in Shopify, but Reconcile.ly is not picking these up, here's why:

Due to the payment not taking place in Shopify, the "Order Paid" event never takes place. (Even though the order is marked as paid).  This means any app, including Reconcile.ly will not be notified of this order.

One way to work around this, would be to change the trigger from when order is paid, to order created within the "Order Settings" of Reconcile.ly

Need more help, feel free to contact us!

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