Nowadays I am doing this way: While doing water change, I completely close the valve on the full siphon line first and then switch off the pump. some amount of water will rush through the trickle/emergency lines at this time. This way the full siphon still have water inside till above the valve, even when the tank water level is below. Once the water change is complete, I switch on the pump first and then once water enters the overflow box, slowly adjust the valve on the siphon line and siphons line comes live in few seconds.
Here, I am talking about my BeanAnimal overflow, with 3 drain lines.