When LA cancelled the SYD AKL part of their flight to SCL a couple of months ago ( I was on the LA flight the next day), I asked the QF people in the SYD Flounge how they managed the rebookings and they said they had LA passengers spread across every available flight SYD AKL in the morning (QF NZ EK etc). They seemed used ro it.
Yes, seems to be a fairly regular occurence cancelling one leg or another. The NZ checkin staff, (they handle all LAN checkins at AKL were telling me they usually put all LAN ticketed pax onto NZ101 (space permitting), and move all QF ticketed codeshare pax onto QF50 which makes sense I guess.