Melt the butter in a small saucepan over medium-low heat. Stir in the brown sugar and cook for 1 minute, until glossy.
Slowly whisk in the milk, then simmer the caramel for 2 minutes, until smooth and slightly thickened. Remove it from the heat and stir in the fine sea salt.
Reserve 3 tablespoons of salted caramel for topping. Let the remaining caramel cool for 10 minutes so it is warm but not hot.
Blend the cottage cheese, Greek yogurt, vanilla protein powder, vanilla, and cooled caramel for 1 to 2 minutes, until silky and thick.
Divide the pudding among four dessert cups and refrigerate for at least 2 hours.
Top each chilled pudding with reserved salted caramel, roasted pecans, and a small pinch of flaky sea salt.