Welcome to FT, cubed2 ^

Unfortunately, what the agent said was true - if any part of a miles upgrade clears (even just a domestic segment) then you are charged the entire number of miles. What you could do is ask that only the LAX-SYD segment be waitlisted for the upgrade - if it clears ahead of time, then you could ask for the JFK-LAX segment to be added to your upgrade request. The problem here, obviously, is that you may no longer be able to upgrade JFK-LAX as upgrade space may have disappeared while you're waiting to upgrade LAX-SYD.

Good luck, at any rate.

You may also wish to think about how badly you want to upgrade. If you value your miles at 2 cents per mile, the cost to you will be $1,000 plus 30,000 x 2 cents, which is $1600. That's pretty steep.