Preheat the Oven: Preheat your oven to 375°F (190°C). Line baking sheets with parchment paper.
Combine Dry Ingredients: In a bowl, whisk together the flour, baking soda, and salt. Set aside.
Cream Butter and Sugars: In a large bowl, using an electric mixer, cream together the butter, granulated sugar, brown sugar, and vanilla extract until light and fluffy. Add the eggs, one at a time, beating well after each addition.
Incorporate Dry Ingredients: Gradually beat in the flour mixture until just combined.
Add Chocolate Chips and Pecans: Stir in the chocolate chips and chopped pecans.
Form Cookies: Drop heaping tablespoonfuls of dough onto the prepared baking sheets. Press a small well into the center of each cookie and fill with a teaspoon of salted caramel sauce. Cover the caramel with a bit of dough if desired.
Bake: Bake for 9 to 11 minutes, or until the edges are golden brown. Remove from the oven and immediately sprinkle with flakey sea salt.
Cool: Allow the cookies to cool on the baking sheets for 5 minutes before transferring them to wire racks to cool completely.
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