Hello Amanda Shafer,
Thank you for your interest in Sitefinity eCommerce module.
Although we are not showing the pnref number on the orders backend, the pnref (Paypal Reference Number) of an order is stored in "gateway_transaction_id" field in the sc_ef_order_payment table.
Also as additional reference, whenever a credit card is processed, the processor returns an "authorization code" that is often given to the customer. This is the "gateway_auth_code" field in the sc_ef_order_payment table (it is not the same as the pnref)
the Telerik team
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