In a medium saucepan, melt the butter over medium heat; bring to a boil. Once the butter starts boiling, swirl the pan constantly until the butter passes the foamy phase and becomes a deep amber color. Remove the pan from the heat and allow the butter to cool for 20 minutes.
Preheat oven to 350 degrees. Line baking sheets with parchment paper; set aside.
In a large bowl, whisk together the flour, baking soda, and sea salt; set aside.
Add the brown sugar, eggs and vanilla the cooled butter in the saucepan and stir to combine. Pour this mixture into the bowl with the flour mixture. Stir using a wooden spoon until the dough comes together. Stir in the butterscotch chips, chocolate chips and pretzels.
Using a medium (2-tablespoon) size cookie scoop, drop the dough 2-inches apart on the baking sheet. Bake for 10-12 minutes until the edges are lightly golden.
Allow the cookies to cool for 2-3 minutes on the baking sheet and then transfer to a wire rack to cool completely. Sprinkle warm cookies with flaked sea salt while cooling.
Store cookies in an airtight container for up to 3 days.