I could be wrong but think there's a system limitation that bags can't go through the same airport twice - for all airlines.
So while CX could/would check trough on separate tickets in general, the system will probably not be able to route through HKG twice.
Edit: read the whole thread now. If it's Just about checking through SYD-HKG-TPE, and then separately, TPE-HKG-XXX at a later time, then there shouldn't be a problem.