I don't see how the separate ticket is relevant. Malindo has an online check-in capability from 48 to 4 hours before your flight. If you have your onward boarding pass before arrival at HKG then there's no problem just going straight through transit security to the departure gate.
Checked baggage would obviously be a problem since you will have to go through immigration to collect your bags and recheck them (because Malindo's short list of interline partners doesn't include CX). For that I would recommend a connecting time of 3 hours minimum.
Terminal 2 is just a separate check-in area, not a separate terminal, but since you should have your onward boarding pass through online check-in then you won't need to check-in again at HKG unless you have checked bags.