The more something is processed, the less nutritious it becomes. There's not really any way around that. The best example I can think of would be oats. It starts out with whole oat groats, then steel cut oats, rolled oats, instant oats, and then oat flour. So the millet flakes will still probably have a fair amount of nutrients in them (I can't say for sure though, I'm not really familiar with millet flakes inparticular). But your best bet is whole millet.