As others have said, I'd say that accurate prediction of the effect on fatigue life will be close to impossible without access to detailed loads information. You'd need a histogram of the different cyclic loads and their frequencies (not easy to derive, even with CFD and FE analysis). That said, I doubt the life of the main flap body is limited by fatigue, especially if it's composite. IT might well be designed to the "endurance limit", below which stress can be assumed not to cause fatigue damage accumulation.