Warm Nutella in a microwave safe bowl for 20–30 seconds, just until thin. Spread in a thin layer on a parchment lined baking sheet and freeze at least 1 hour or overnight.
Once frozen, cut Nutella into squares or rectangles and refreeze for 30 minutes.
Preheat oven to 375°F and line baking sheets with parchment paper.
In a stand mixer, cream butter and sugars until smooth, 2–3 minutes.
Add eggs and vanilla, mixing well and scraping down the bowl.
Add flour, baking soda, baking powder, and sea salt. Mix until just combined.
Stir in chocolate chips.
Gently fold in frozen Nutella chunks.
Scoop dough using a 3 tablespoon scoop onto prepared baking sheets, spacing cookies about 2 inches apart. Keep remaining dough chilled between batches.
Bake for 10–12 minutes, until edges are lightly golden and centers look slightly underbaked.
Sprinkle with flaky sea salt while warm and cool slightly before serving.