I just looked at the recipe. I see what you mean, you're looking to make it a little more "healthy breakfast cookie" instead of "healthy dessert cookie". Right?
I think a half cup of flax would make the cookies fall apart. I don't think the eggs would be able to bind that much together. If you need a little more fiber in them, go for 2 tablespoons of flax MEAL (grind your flax seeds in a spice grinder or coffee grinder) and mix with the batter. I think any more than that and you're going to run into problems with the cookie crumbling.
If portable is what you need, have you tried the egg cups? It's basically scrambled eggs in a muffin shape. There is a recipe in the breakfast section, but you can add anything you want. My husband isn't a big fan of turkey bacon, so we either omit the meal entirely or use turkey italian sausage. I fill it with sauteed veggies (peppers, onions, zucchini, spinach, etc.)
100 lbs. down plus a carrot for every 5 more