Yes. I have done this twice.
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Looks like it is moot point now, I believe there's availability on PER-SYD for the 12.30 flight next Thursday, but not the 16.30 which is the one I'd be looking to take.
12.30 is A330 so more seats available than the 16.30 which is 737. Never had a problem upgrading on the A330.
If you're booked on a flexi fare with a connection, does an upgrade request allow both segments to be upgraded to J? Eg, BNE-SYD-PER. What will the the cost of the upgrade then? Equivalent to BNE-PER or, BNE-SYD + SYD-PER?