Making Whole Grain Rustic Bread

After reading the article about white versus wheat bread and learning about the importance of leaving the grain in it’s form raises a question for me. Recently I started making my own ‘multi-grain’ bread. I have been using wheat berries, quinoa, and flaxseed and processing them in a high speed blender to create my own flour. I have been stirring in whole flax seeds and oatmeal into the dough. Am I loosing nutritional value by processing the grains into a flour? What are your suggestions to modify my recipe to keep this a healthier choice?