Refunds for orders that are processed in ToGo need to be refunded on OrderCloud. The payments are made on OrderCloud and the credit card information is not sent to the POS. Refund on the POS will only adjust your sales numbers, the actual refund back to the customers card need to be performed in OrderCloud.
The only exception to this is for locations with an integrated Square POS. In this case, Square is the credit card processor, so you will refund orders from your Square account as if it were an in-store purchase.