PNR is just a reservation number. The actual purchase is the ticket. Until the eticket is issued there is no confirmed purchase. There are many cases of problem between airlines systems. Without a ticket in hand, there is little that one can do, unless the metal airline shows some goodwill.

Unfortunately relations between CX and QR are not excellent, despite QR being a CX shareholder. QR would now have to force CX to open award space for them.

Maybe a comparison would be: you order some good from your local store who takes the money. Then the store advises you that their supplier does not have that good anymore and refund the money.