CRK advises against flicking mostly as a disclaimer.
In an email response to a previous poster, they state explicitly that flicking your knife on occasion is fine, and even encouraged since it helps the lock to set. Flicking your knife compulsively and ceaselessly, while watching TV for instance, will eventually inflict due wear on the stop pin, and this is true of every knife, whether the manufacturer indicates it or not. You think flicking open your Benchmade all the time is going to be any less destructive just because Benchmade doesn't say anything about it? The rotating stop pin on a Sebenza goes a long ways toward reducing precisely this kind of wear, but no knife on earth can dispel it completely.
Flicking a knife, any knife, will eventually wear it out. It's just a matter of time. The Sebenza actually resists this kind of damage better than most knives, due to the quality of materials and design, but no knife lasts forever. If you are moderate in your flicking activity, most knives will never give you trouble, but if you do it hundreds of times a day for its own sake, you reduce the possibility that the knife will outlast you.
Simple as that.