With a flush, you change ALL the fluid.
This is how I did it:
Basically, jack up the car, and open the bleed nipple. The fluid will just drain out (very slowly). When the master cylinder reservoir is empty, fill with the replacement fluid. Then open each nipple individually, and allow to drain until the new fluid starts coming out (obviously easier if new / old fluids are different colours). ie open LR, drain, close, open RR, drain, close, etc.
Once all calipers are running new fluid, do a normal bleed to clear any air from the system.