if it is recomended to flush, i say flush, let the rain fall, but a flush is more than rain, you are trying to get rid of the nute build up i assume? so flush. i think it means like three gallons of water for every gallon of soil. i flush mine before harvest, or if i have nute problems. So flush and let that sweet rain fall.
oh yeah, the root rot wont happen if you have adequate drainage...