In a medium bowl, whisk together the gluten free flour, both cocoa powders, the baking soda and the kosher salt. Set aside.
In a small bowl, using a spoon, mix together the cornstarch and water until thin and watery. It will be thick and tacky at first. Set aside.
In a large bowl of an electric mixer fitted with the paddle attachment or using a hand held mixer, beat the room temperature butter or vegan baking stick and the dark brown sugar until soft and creamy. About 2-3 minutes.
With the mixer on low speed, beat in the cornstarch water mixture. Then beat in the vanilla, molasses and milk. The mixture might look slightly chunky and that’s ok.
Still on low speed, beat the gluten free flour mixture into the wet ingredients, a little at a time until just combined.
Once combined, scrape down the sides of the bowl with a spatula and using the spatula, fold in ¾ cup of the chocolate chips.
The batter will be very wet and sticky. Don’t try to take it out of the bowl. Cover the bowl with plastic wrap and put it in the fridge for at least 2.5 hours. It needs to harden otherwise the cookies will spread all over the place.
After 2.5 hours, preheat the oven to 325 degrees Fahrenheit. Line a baking sheet with parchment paper. Set aside.
Take the bowl of dough out of the fridge. Using an ice cream scoop, scoop the dough out. At this point the dough will still be a bit sticky. There should be 12 scoops.
Place the additional ½ cup of chocolate chips on a plate.
Press the top of the dough balls into the chips. Gently press so the chips stay in the dough.
Place the dough balls on the baking sheet about 3-4 inches apart. I only put about 6 cookies on the tray at a time. Put the extra dough back into the fridge in between batches.
Bake the cookies in the middle rack for 13-15 minutes.
Take out the cookies and immediately use a spatula to reshape your cookies if they spread a bit.
After reshaping, let the cookies cool on the baking sheet for an additional 5 min after removing them from the oven. If you try to take them off too soon, they will break apart.
After 5 minutes, transfer them to a cooling rack.
Repeat this entire process with the rest of the dough.