My guess is that by changing the BNE-SYD flight you are in effect changing the booking class for the entire journey. The originally offered flights (incl 5:00am BNE-SYD) may have all been available in say N class. But the 5:00pm BNE-SYD is not available in N class and the cheapest for that sector may be say M class. So its now repricing the entire journey as M class (perhaps the fare rules for the N class fare does not permitted mixed class ticketing). Hence the extra $379 is not just the extra price for BNE-SYD, but the additional cost of the entire journey in the higher class.
Then when you change back to the 5:00am flight, the system is retaining the higher booking class (e.g. M in my example) rather than repricing back to the lowest booking class that would be applicable for the journey.
I am not suggesting this is how the system shoudl work, just posing a possible explanation as to why you are seeing this behavior.