How can I export the Shopify "Payment Reference" data?
In Shopify's default CSV export, there's a column called "Payment Reference" which is essentially the checkout ID and often used in reconciliation.
In EZ Exporter, you can retrieve this data by selecting the field called checkout_id in the Data Settings for order exports.
One thing to note is in Shopify's CSV, they put a "c" in front of the checkout ID and a ".1" (or ".2", ".3", etc) at the end. The ".1" is basically the number of attempts to a successful transaction. However, the Shopify API only provides the numbers so that's all you will see in EZ Exporter's output.
App: EZ Exporter