In a large bowl, whisk together the white whole wheat flour, all-purpose flour, cornstarch, baking powder, baking soda, and salt. Set aside.
In another large bowl, beat together the coconut oil, granulated sugar, and brown sugar on medium speed until well combined and smooth, about 3 minutes, stopping to scrape down the bowl once or twice. Scrape down the bowl again, then add the egg, milk, and vanilla, and beat until combined. Reduce the mixer speed to low, then slowly add the dry ingredients, beating just until the flour disappears. By hand, fold in the chocolate chips. Cover the dough and chill for at least 4 hours or overnight. (For a shorter chilling time, shape the dough into cookie balls and arrange in a single layer on a cookie sheet or plate and place in the refrigerator for 2 hours.)
When ready to bake, remove the dough from the refrigerator and preheat your oven to 375 degrees F. Line a baking sheet with parchment paper or a silpat mat. With a spoon or scoop, portion the dough into small 1 1/4-inch balls and place on the prepared baking sheet, leaving 2 inches between each. Bake the cookies for 7 minutes, until the edges are barely golden brown. They will look underdone, but resist the urge to continue baking. Remove the pan from the oven and place on a wire rack. Let the cookies cool for 5 minutes on the baking sheet, then transfer them to the rack to cool completely.
Leftover baked chocolate chip coconut oil cookies can be stored in an airtight container at room temperature for up to 5 days or frozen, well-wrapped, for up to 3 months. Frozen cookie dough balls can be baked directly from frozen—do not thaw and simply add 1 to 2 minutes to the baking time.
If baking multiple batches on the same baking sheet, let the sheet cool completely between batches or the cookies will spread.