Flushing will generally remove some of the N from organic soil mixes - not as much, but some. The key, which takes experimenting to get right, is to put in just the right amount of N at the beginning of the grow so that it is tapering off a touch toward the end of the grow. This also means you don't want to be giving the plants any supplemental N during flowering, unless it's early and they are clearly needing it.
For this time I would flush them out pretty good, maybe even twice about a week apart, and you probably won't have much of a problem. For future grows you can start figuring out the optimal amount to feed them, and you'll probably start cutting back on the amount of supplemental feeding. Remember if you have a good solid soil mix, like say good quality potting soil amended with compost and worm castings, you won't need much in the way of extra nutrients.
I did hear of one horror story where a guy grew in a soilless medium and used guano and I think fish emulsion as the liquid ferts, didn't flush, and the bud tasted like creamed corn. Mmm-mmm-gross.
Then again he didn't have soil to buffer the effects, so you shouldn't worry too much.
O