I don’t understand the “Payment Reference” property you are looking for. If you bring up an order in the admin web UI, you can just append .json to the end of the address your the browser address bar. For example:
This will show the raw JSON data for the order. If you look in there you should see payment_gateway_names, which shows the route that the payment was processed. You should also see payment_details, which contains the properties for the payment (e.g. - credit card details).
Thank You for Your time, I believe You are correct, but please take look at my example.
On right You can see order export, with payment reference #1003.1 on left side there is transactions array for it (You can cross compare field ID and order_id it’s missing payment transactions (because this is test payment) but still it have #1003.1 id filled in CSV?

I’d suspect this was because it was a manual/test transaction. When the shop is connected with a payment gateway and whatnot in production I’d imagine that the Transactions endpoint would indeed provide you with what you are looking for. If anyone else would like to chime in as well to confirm
I don’t recall anything special. Just hitting the API endpoint and looking at the response body. Then in the Shopify web admin I would pull up a specific order, and just append .json to the URL to view the raw data. The only thing I remember is that perhaps test transactions that didn’t hit a real payment gateway wouldn’t have all of the data properties that a real transaction would…
In the end, it is impossible after the fact to update a transaction in Authorize.net with the proper Shopify Receipt. The only real solution is for Shopify to admit they have it wrong and fix it. It would take seconds to fix. I can’t believe all of their users just tolerate this.