These are truly the Best Chocolate Chip Cookies EVER! The time and effort it takes to make these chewy, soft-baked chocolate chip cookies will be WELL worth it!
In a large bowl, sift together flours, baking soda, baking powder and salt. Set aside.
Using a stand mixer fitted with the paddle attachment, cream together the butter and sugars until very light, about 5 minutes. Add the eggs, one at a time, mixing well after each addition. Mix in the vanilla and mix until vanilla is gone. Reduce the speed to low and slowly add the dry ingredients and mix until just combined. About 10-15 seconds. Drop in chocolate pieces and incorporate them without breaking them. You might need to take the bowl off the stand and just fold it in by hand (which is what I did).
Take large piece of plastic wrap and lay it on the counter top. Put the dough on top and wrap the dough up in the plastic wrap.
Refrigerate for 24 to 36 hours.
When ready to bake, preheat oven to 350 °F (177 °C). Line baking sheets with parchment paper or silicone baking mats. Set aside. While the oven is pre-heating, set your dough out to warm up a little.
Using your hands, break off the dough (it'll be kinda hard) into two tablespoon pieces and roll into balls. Place them two inches apart on the baking sheet.
Bake the cookies for 18-20 minutes or until golden brown but still soft. Allow the cookies to rest for 5 minutes before transferring to a wire rack to cool completely. Sprinkle sea salt flakes on top.
Repeat with remaining dough or you can reserve the remaining dough by freezing it.