Preheat an oven to 375°F, and set an oven rack in the middle position. Line a baking sheet with parchment paper and set aside.
In a medium bowl, whisk together flour, baking soda and salt. Set aside.
Add the butter and shortening to the bowl of a stand mixer fitted with the paddle attachment. Beat at medium speed until creamy, then gradually add the sugars, beating until fluffy (3 - 4 minutes more). Beat in the eggs and vanilla until fully incorporated. In 3 additions, beat in the flour mixture until just incorporated (start the mixer slow, then increase to medium speed each time). Don't overmix here. Stir in chocolate chips and chopped pecans.
Using a 1/4 measuring cup, drop cookie dough on the prepared baking sheet at least 3-inches apart (I like to do 6 per sheet). Sprinkle each mound of dough with a little flaky sea salt. Working in batches, bake until the cookies are lightly golden brown (11 - 13 minutes). Let cookies cool on the baking sheet for 2 minutes, then transfer to a wire rack to cool completely.