In a small bowl, make the flax egg by combining the ground flaxseed and water. Stir and set aside for 5 minutes to thicken.
In a large bowl, add the flour, baking soda, and salt. Whisk until combined.
In the mixing bowl of your stand up mixer (I used my KitchenAid), add the coconut oil, brown sugar, cane sugar, miso, and milk. Cream together with the paddle attachment until light and fluffy, about 2-3 minutes. Add the flax egg and vanilla extract. Cream together for 1 minute.
Slowly add the flour and mix on low until incorporated. Add the chocolate chunks/chips and pulse the dough until combined.
Use a large cookie scoop (about 2.5-3 tablespoons) and scoop out dough and roll into balls. Place onto a lined baking sheet or plate. I got about 12 big cookie dough balls. Cover with plastic wrap and place in the fridge for at least one hour or overnight (I did overnight).
When ready to bake, preheat oven to 350 degrees F. Line 2 baking sheets with parchment paper or a silicone mat. Place 6 dough balls on each sheet. Bake one sheet at a time for 12-14 minutes, or until edges are golden brown. Take out of the oven and lightly drop the sheet on the counter a few times. Let it cool on the pan for 10-15 minutes. Sprinkle with flaky sea salt and enjoy!