In a large bowl, whisk flours, baking soda, baking powder, and coarse salt. Set aside.
In the bowl of an electric mixer fitted with a paddle attachment, cream butter and sugars together until light and fluffy, about 5 minutes.
Add eggs one at a time, mixing well after each one.
Stir in the vanilla and mix thoroughly, scraping down the sides of the bowl as needed.
Reduce speed to low. Add the flour mixture and mix until just combined, 5- 10 seconds. Do not over mix!
Add chocolate to the dough and evenly incorporate with a spatula.
Press plastic wrap against the surface of the dough and refrigerate for 24-36 hours (I'd go for 36 hours), up to 72 hours.
After the resting period, allow chilled dough to sit out at room temperature for 30-60 minutes or until it's softened enough to scoop.
When ready to bake, preheat oven to 350°F.
Scoop 6 mounds of dough onto a parchment-lined baking sheet. I used a #20 scooper which is approximately 3 tbsp.
Sprinkle with flaky sea salt and bake 11-13 minutes. The middle should look soft and the edges should be golden brown.
Remove from oven and let cool for 5 minutes before transferring cookies onto a wire rack. Repeat with remaining dough, or reserve dough for baking next day.