OK, another 30 mins on the blower to Qantas, got a more knowledgeable agent this time who as soon as I mentioned they'd cancelled our BNE-SYD flight, knew that it was QF's responsibility to reaccommodate us on a flight that worked for us. She has sorted it out, linked our bookings, and reticketed.
She was even trying to get our seats closer together, but we were already pretty happy with not sitting next to each other.
OH and she said she'd pass feedback to the original agent I spoke to about this situation and what they should be able to do.