Combine dry flour, baking soda, baking powder and salt in a large bowl. Whisk to combine and set aside.
In the large bowl of a mixer with the paddle attachment in place, add the butter, coconut oil, brown sugar, and granulated sugar. Cream on medium speed until it’s nice and fluffy. This might take 3+ minutes. Then add the applesauce and vanilla. Mix until well combined.
With the mixer running on low speed, gradually add the flour mixture. Mix until just incorporated. Add the chocolate chips and mix in. Cover the bowl with plastic wrap and chill for 24 hours.
Remove dough from the refrigerator and let it soften a bit. Line a baking sheet or two with parchment paper and preheat your oven to 350 F. Using a ice cream scoop, scoop about 1/3 cup of dough and form into a ball. Place on the parchment paper and flatten with your fingers or the back of a measuring cup. Sprinkle lightly with flake salt.
Bake cookies for 12-14 minutes, depending on how crispy you like your cookies. Transfer cookies to a wire rack to cool.