My apologies, I neglected to see that you were in Australia when I read your first post. I do not know Australian electrical code, nor do I know the nomenclature. I can tell you how a 3-way switching system works, and perhaps you could use that information to figure out what you need to do.
A 3-way switch has two positions, call them A and B. Note that these positions are NOT on and off, just A and B. A and B are two different paths for the electricity to flow. Either A or B will allow the electricity to flow, but both switches must be in the same position for this to happen. Changing either switch will open the circuit and stop current flow.
A 3-way switch has three terminals. One is called the common and the other two are called travelers. When power comes into the first switch, it is connected to the common terminal. Then one wire is connected to each of the traveler terminals and leaves the switch box. They go directly to the second 3-way switch. They can stop inside other boxes and be spliced if necessary, but they cannot be interrupted. They must go from one switch to the other. When they get to the second 3-way, they go on the traveler terminals of that switch. Then a wire is connected to the common of the second 3-way switch, and this wire goes to the light fixture. This is called the switch leg. Out of the light fixture comes the neutral, and this goes back to the panel.
When you took the old fixture down, how did the wires look inside the box? Were there splices? For example, were the two neutral wires spliced with a third shor piece of neutral wire that went onto the terminal of the fixture? Was this the case with the ground and or/hot (active)? Is this a double pole breaker? Again, I apologize but I'm still having difficulty picturing what you have in your home. Perhaps a trip to your local home store might be in order. Do they give advice and answer questions in those stores?