Spread pecans on a dry baking sheet and toast at 350°F for 8-10 minutes until fragrant and slightly darkened. Let cool, then roughly chop. Keep the oven on for baking.

Melt butter in a medium saucepan over medium heat, swirling occasionally. Continue cooking 3-4 minutes until the foam subsides and you see golden-brown bits on the bottom. It will smell nutty and caramel-like. Immediately pour into a large heatproof bowl, scraping in all the brown bits. Let cool 10 minutes until warm but not hot.

Whisk both sugars and maple syrup into the warm brown butter until well combined. Whisk in the egg, egg yolk, and vanilla until glossy and smooth, about 30 seconds. Add the flour, baking soda, and salt, then stir with a wooden spoon just until no dry streaks remain. Fold in the toasted pecans and chocolate chips. The dough will be soft and slightly sticky.

Cover the bowl and chill dough for 20 minutes while you line two baking sheets with parchment. This firms up the butter and prevents spreading.

Scoop 2-tablespoon portions of dough onto prepared sheets, spacing 2 inches apart. Bake one sheet at a time at 350°F for 12-14 minutes, until edges are set and centers look slightly underdone. The cookies will puff, then settle into crinkled tops.

Immediately sprinkle each warm cookie with flaky salt. Cool on the sheet for 5 minutes, then transfer to a wire rack. Cookies firm up as they cool but stay chewy for days.