It seems the particular agent isn't aware of the 're-zoning' of the BKK-KUL flights. Your correspondence needs to outline that although the points and status credits were applied at the time of travel, Qantas has subsequently determined those points and staus credits were incorrect and did not accurately reflect the class of travel, fare, carrier and miles flown.
As Qantas has now correctly determined the class of travel, fare, carrier, and miles flown, you are seeking your balance to updated accordingly. (You could also note this is only a recent correction by Qantas and wasn't able to be acted upon by passengers until Qantas had worked out the correct points and stats credits to be applied to the route.)
If that doesn't work, it could be a good case for the Airline Consumer Advocate.