I don't know how Qantas booking system exactly works. But I feel sorry for the OP.
My understanding is the initial booking was a return trip and both legs are in the same PNR, and OP would like to change only one leg to a different date and keep the rest unchanged. This could trigger the whole mess, as most Airlines rewards bookings do not allow partials change within one PNR, unless the whole trip get rebooked. In this case, I guess the agent never (or not able to) split the booking, instead, canceled the whole booking straight way. The agent should be more acknowledged for the solution, really should suggest to create a new booking first before amend any existing one.