In a medium bowl, whisk together the flours, cocoa powder, baking soda, and salt and set aside.
In a stand mixer, cream together the butter and both sugars on a low speed until combined. Scrape the bowl down once or twice as needed. Add the molasses (or corn syrup) and beat until combined.
Add the eggs one at a time, mixing on low just until combined after each. Add the vanilla. Beat until combined. Scrape the bowl down as needed.
Add the dry ingredients to the wet and mix on low until just combined. Add the chocolate chips. Mix on low until combined. It should just take a few seconds.
Use a cookie scoop to portion the dough and place onto a tray or baking sheet lined with parchment paper. Repeat with the remaining cookie dough.
Place the trays in the freezer for about one hour. Transfer the frozen cookie dough balls to a freezer bag or airtight container. Freeze for at least 4 hours, but preferably overnight.
When you are ready to bake, preheat the oven to 325°F. Place frozen cookie dough balls on a baking sheet lined with a silicone baking mat or parchment paper. Bake for 20 minutes or until the edges of the cookie are set, but the center is still soft.
Let them cool on the baking sheet for 5- 10 minutes before transferring them to a cooling rack.
After the cookies have cooled, gently melt the 2 oz of chocolate and drizzle over the cookies. Before the chocolate sets, sprinkle with flaky sea salt.