I just ran into this problem today. I am on a QF BC award ticket SIN-MEL-SYD-SIN. I called Cathay Pacific who issued the award to check whether I could skip or cancel the MEL-SYD segment without having the SYD-SIN segment canceled. They said no but check with QF. I checked and QF said it couldn't be done - it's considered a change in routing.

It's crazy - QF could have saved me flying a BC segment at whatever cost it is or better yet made it available for QF frequent flyer awards or upgrades.

I must say that my QF award ticket has caused me a lot more trouble than I ever expected. I usually fly on Northwest awards and they are much more flexible.