Energy can be stored in the flex or in the potential energy of lift the riders CG higher. The question is whether this stored energy is later returned usefully or dissopated through other mechanisms (damping being one possibility). You can bounce up and down in place on your legs or on a pogo stick and expend a lot of energy without going anywhere. Similarly you can expend a lot of energy accomplishing no useful work lifting weights at the gym or by flexing the springs in a Bowflex. With flex in a bike, some of the stored energy may be returned usefully but some is certainly lost.