I used to flush for 5-10 mins once a week, but now i dont really see the reason for it so dont really bother . However when i first switch it on, i have a bypass just before the di vessel to let the first litre or so of pure not go through the DI and into the ibc as it takes about a minute for the membrane to bring the water to as low as it can.
For me personally when i first switch it on the pure water going to the ibc starts off at about 120 ppm and gets down to about 14ppm after about a minute thats when i then let it go into the DI vessel.