In a medium saucepan over medium-low heat, melt butter. Once completely melted, add sugars and turn off heat. Whisk or stir until butter-sugar mixture looks glossy and smooth - about 2 minutes.
Let cool to room temperature. May leave out at room temperature until cool or place in refrigerator for 5-7 minutes. You don't want it to be hot when adding the eggs. Add egg, egg yolk, and vanilla and stir well to combine.
Fold in flour, baking soda, and salt until just combined. Fold in semi-sweet and milk chocolate chunks.
Wrap dough in plastic and refrigerate until firm, about 30 minutes. For richer, toffee flavored cookies, let the dough chill for 24-36 hours.
Preheat oven to 325 degrees.
Place golf ball size mounds of cookie dough on baking sheets. Bake until cookies are golden brown, 12-14 minutes. Sprinkle with sea salt flakes. Allow cookies to set for 5 minutes before transferring them to wire rack.