Preheat the oven to 350 degrees F.
In a medium bowl, stir together the flour, cocoa powder, baking soda and salt. Set aside.
In a large mixing bowl or the bowl of a stand mixer, combine the butter, shortening, sugar, brown sugar, eggs and vanilla extract and beat on medium-low speed until mixed with just small chunks of butter remaining, approximately 30 seconds. Every time you mix incredients, scrape down the sides of the bowl with a spatula to be sure all ingredients are included in the mix.
Add half the dry ingredient mixture and mix on low speed until incorporated and all butter chunks are gone, approximately 20 seconds. Add the remaining dry ingredients and mix until the dough pulls away from the sides of the bowl and is not sticky to the touch, about 20 seconds.
Stir in the chocolate chips.
Line two baking sheets with parchment paper.
Scoop the dough 1/3 cup at a time and firmly roll into round balls approximately 1 1/2″ in diameter. Place six cookies on each prepared baking sheet, spacing them out well.
Top with sea salt flakes, if desired.
Bake on the middle and lower racks of the oven until you notice hairline cracks forming on the sides, 12 to 14 minutes, spinning each pan 180 degrees and swapping their positions halfway through.
Let cookies cook on the baking sheets for 10 minutes, then use a wide spatula to transfer them to a wire rack to cool completely. Let baking sheets cool before repeating with the remaining cookies.
Store in an airtight container at room temperature for up to 4 days or freeze for up to a month.