I can agree with the fact 15below thinks a dummy passive segment is a live segment and therefore comms being sent accordingly being a system limitation.
However, your live seats were likely cancelled as part of the refund process triggered by your unauthorised charge chargeback request to Amex. It is common for airlines to replace the live seats with dummy passive segments for the same flights so there is a record of what the itinerary was.
If the live seats were indeed cancelled as part of the refund process, then at near departure, nothing could have changed as far as paying for a new redemption ticket as there would have been no live seats in the PNR to issue a ticket against. Assuming this is the case, then the airline was correct to require you to pay for a new set of commercial fares in order to travel.
If the live seats were still in the PNR, then there is no technical reason that they couldn't have just issued a new redemption ticket in the same PNR. If this was the case then I'm of the opinion they should've simply issued a new redemption ticket and allowed you to travel, providing you had sufficient spare miles in your account for a brand new charge of miles as the previous set of used miles would've still been tied to the old ticket that was refunded by chargeback.
That said, I would also agree with a stance that the booking is considered dead/refunded/no longer usable if they wanted to go with this, as you did do the chargeback in the first place. If CX took this stance, I would say they're well within their right to.
