First, preheat your oven to 350°F/177°C and then prep two baking sheets by lining both with parchment paper.
Combine the flaxseed and water in a small bowl and set aside.
In a mixing bowl, whisk together the flours, sugars, cocoa powder, baking powder, baking soda, and salt, breaking up the sugar and flour clumps along the way.
Add the oil, peppermint extract, the flaxseed mixture, and the chocolate chunks and stir until all the flour is incorporated. The dough will be very thick.
Divide the cookie dough into 12–13 equal-sized balls and place them on parchment-lined or ungreased baking sheets 3 inches apart from one another. Bake in your preheated oven for 12–13 minutes or until the surface of the cookies is matte rather than shiny. It's better to slightly underbake than to over bake.
Immediately upon removal from the oven and while the cookies are still on the baking sheets, top each cookie with the candy pieces and lightly press down so they stick to the cookies' surface.