Well I just rang VS, got through straight away on the special number that I was given.
My Sydney to Hong Kong and return sectors have been booked onto QANTAS in business class and for my wife's award ticket from LHR-SYD, she's been booked onto QANTAS as well and she's even on the same flight as me
My only concern is that with our luggage we may have to collect it and re-checkin at Hong Kong for our connecting flights. I'm not sure there's a VS/QF interline agreement in place.
At least it's been sorted and it was done very quickly on the phone. I was told it will take about 48 hours for the re-issue of the tickets.
For the future I just have to think how I can use the remaining points in my FF account!