I had a similar experience in Brisbane a few months ago. I was on a points trip with a multi-stopover itinerary.

Half-way through my trip, I needed to change my routing and go through Sydney. I had already stopped in Sydney twice on that trip and the rule is two is the limit.

But they were very helpful in Brisbane and they changed my routing on the spot and charged no extra points, letting me go through Sydney three times on one points ticket.