Chapati flour, also called Atta, is not exactly the same as supermarket brand whole wheat flour. In fact, the Chapati flour is milled somewhere between the whole wheat and the all-purpose. So, actually the supermarket brand whole wheat makes a more thick chapati because the flour is more coarse. And if you ever happen to be at an Asian grocery store and see Indian Chapati flour, buy it! I promise you will remember them forever. It does make a difference. And no, the flour won't go to waste - you can make bread with the leftover.