Well just got off the phone with Qantas, think it may have been the Manilla call centre, he sounded Filipino and seemed decent.
Anyway after he spoke with his support team (or whoever), they actually have opened up two business seats on the LAX>MEL flight for me which I sort of couldn't believe. The flight and correct cabin class is now reflected in the booking on the Qantas site/app. He said the new ticket will be issued within 24hrs and the other partner airline flights are not in limbo and are 100% locked in still and unaffected.
If I don't have the ticket by tomorrow morning I will call up and start to get pushy just to get it over the line.