Line two cookie sheets with parchment paper.
Combine the all purpose flour, rye flour, baking soda and salt in a medium bowl and whisk to combine.
1 cup all purpose flour, 1 cup rye flour, ½ teaspoon baking soda, ½ teaspoon fine sea salt
Melt the butter in the microwave in 30 second increments until fully melted. Cool to room temperature. Pour the melted butter into the bowl of a stand mixer.
¾ cup unsalted butter
To the butter, add the brown sugar and granulated sugar. Beat to combine, 1-2 minutes.
⅔ cup dark brown sugar, ½ cup granulated sugar
Beat in the bourbon, vanilla, egg and the egg yolk, and beat until well combined, about a minute.
1 tablespoon bourbon, 2 teaspoons pure vanilla extract, 1 large egg, 1 large egg yolk
Beat in the flour mixture and chocolate and mix on low speed until just combined.
1 cup bittersweet chocolate, chopped
Cover the bowl with plastic wrap and chill the dough for at least 4 hours or overnight.
Preheat the oven to 350F. Line two cookie sheets with parchment paper.
Using a medium size, 2 tablespoon ice cream scoop, scoop out the dough onto the cookie sheets leaving 3" between each cookie.
Sprinkle the tops of the dough balls with flaky salt. Bake for 12-14 minutes or until the edges are lightly brown and the tops look just set.
flaky salt for sprinkling
Cool on the cookie sheets for 5 minutes before transferring the cookies with wire racks to cool. Serve warm.