Can someone explain how the money trail works?

I suppose it is an AC ticket (014?) for the entire trip? If the OP paid AC and CX takes the J coupon through ARC. Would CX end up with the J money?

Strange that the AC segments did not cancel - they don't require TKNO?

Once the PNR rolls off the reservation system, is there an easy way for the first line people to pull up the history?

Would disputing with the credit card company help? Paid J and got Y, sounds like you can try that too.