Preheat the oven to 350°F (175°C) and line a baking sheet with parchment paper.
In a medium bowl, whisk together the flour, baking soda, baking powder, kosher salt, and cinnamon.
In a large bowl, combine the melted, cooled butter, brown sugar, and granulated sugar. Beat for about 3 minutes until the mixture thickens and becomes lighter.
Mix in the egg and vanilla extract until smooth.
Add the dry ingredients and mix until just combined. Fold in the semisweet chocolate chips, butterscotch chips, and chopped pecans.
Scoop the dough into approximately 15 portions, using about 2 tablespoons of dough per cookie. Arrange them several inches apart on the prepared baking sheet.
Bake for 10–12 minutes, until the edges are lightly golden while the centers still look slightly pale and soft.
Sprinkle with flaky sea salt while the cookies are warm. Let them rest briefly on the baking sheet before transferring to a wire rack to cool. Serve.