In a medium bowl, whisk together the flour, baking soda and salt and set aside. In a small saucepan or microwave, melt the butter. Stir in both sugars and whisk until smooth. Add the egg yolks and vanilla and whisk again. Pour the butter mixture into the flour mixture and stir until just combined. While the mixture is still warm, fold in half a cup of the chocolate and stir. Let the mixture cool a bit and then add the remaining chocolate and pecans. The dough will be very loose. Cover the bowl with plastic wrap and chill until the dough is firm, several hours or overnight.

Pre-heat the oven to 325°F and position a rack in the center of the oven. Let the dough soften a few minutes while the oven is pre-heating. Line two baking sheets with silicon pads or parchment paper. Roll the dough with your hands into golf-ball size chunks, placing them on the baking sheets about 3 inches apart.

Bake the cookies for about 10-12 minutes. Remove from oven, sprinkle sparingly with flaky salt. Cool on the baking sheets for 2 to 3 minutes, and transfer to a wire rack.