I'm no great expert, but it might depend on how you're travelling from BNE to SYD.

From ADL, if flying QF to MEL or SYD then onwards with CX, QF will only give you the QF boarding pass, and you need to get your CX passes (all of them) from CX check-in at MEL/SYD.

Not sure if the same is true for BNE.

But you should have no problems with getting the ICN boarding pass wherever in Australia you first check with CX.