Preheat oven to 325 degrees F. Line baking sheets with parchment paper and set aside.
Combine flour, baking soda, and salt in a medium bowl. Set aside.
In the bowl of a stand mixer, beat the butter for 30 seconds until smooth. Add cookie butter and sugars, and cream for 2 minutes until fluffy. Add the egg, egg yolk, and vanilla and mix well.
Gradually add flour and mix until a crumbly dough forms. Fold in chocolate chips. Cover the bowl with plastic wrap and refrigerate for 30 minutes - 24 hours.
When ready to bake, use your hands to shape tablespoons of dough into balls. Place on prepared baking sheets, two inches apart, then sprinkle each with a bit of sea salt.
Bake for 10-12 minutes or until the edges begin to brown, but the centers remain soft and puffy - do not over bake! Remove from oven and allow to cool on baking sheets 5 minutes, then move to cooling rack.