Can I refund an eCommerce credit card transaction with a different payment method? In other words, can I refund a $50 eCommerce Visa credit card payment with a $50 check?

Yes, you are able to use the Refund by Different Payment Method button to issue the refund with a different method of payment. This refund transaction will not be sent to the gateway and will not be put onto the credit card. See Refund a Settled Credit Card Payment with a Different Payment Method. Please note that refunding a payment that was originally made with a credit card, by any means other than back to that card, is against Visa/MC regulations and as such this is not a Jackrabbit recommended Best Practice.