Preheat oven to 350 degrees F. In a large bowl beat butter with a mixer on medium to high 30 seconds. Add both sugars, baking soda, and salt. Beat on medium 2 minutes, scraping bowl as needed. Beat in eggs, orange zest, and vanilla. Add melted chocolate; beat until combined. Beat in whole wheat flour and flax meal. Beat in as much of the all-purpose flour as you can with the mixer. Stir in any remaining flour. Stir in chocolate chunks and pecans.
Drop dough by tablespoons 2 inches apart onto ungreased cookie sheets. Bake 9 to 11 minutes or until puffed and tops are just set (do not overbake). Cool on cookie sheet 2 minutes. Remove; cool on wire racks.