Originally Posted by
wheresmybagba
However when I called up QF and asked them to do that for me they told me...computer says no! Or more accurately....'we don't do that anymore we have a new system, goodbye'.

This partially true. When the switch was made to the new Altea system it was found the CIA were not able to see some cross-referenced PNRs. That is, despite having been linked through the phone centre, the connection was not being shown in the booking page at check-in rendering it redundant.
Just provide the CIA with both booking references and let them know you wish to be thru-checked to your final destination.