Preheat oven to 350 degrees F. Line a baking sheet with parchment paper or Silpat baking mat or parchment paper. Set aside.
In a medium bowl, whisk together flour, baking soda, sea salt, and cocoa. Set aside.
With a mixer, cream butter and sugars together until smooth. Add in eggs, one at a time. Next, add in vanilla extract and mix until combined.
Gradually add flour mixture and beat until just combined. Stir in the 1 cup of chocolate chips and 1 cup of chocolate chunks. Scoop the dough into rounded tablespoons and place on prepared baking sheet, about 2 inches apart.
Bake cookies for 8 minutes and remove the baking sheet from the oven. Quickly press the chocolate wafers or big chocolate chunks gently into the tops of the cookies. Place the baking sheet back in the oven and finish baking the cookies for an additional 2 minutes or until the cookies are set around the edges but still soft in the center.
Remove from oven and sprinkle the cookies with flaky sea salt. Let the cookies sit on the baking sheet for 3 minutes. Move to a cooling rack and cool completely.
You can freeze the baked cookies or freeze the cookie dough balls, for up to 3 months.