Place 1 bag chocolate chips in a microwave safe bowl, then heat in 30 second increments, stirring after each, until completely melted and smooth.
Line a mini muffin pan with muffin liners. Take 1 heaping tablespoon of melted chocolate and pour it into prepared muffin tin. Use a small spoon to push chocolate up the sides of the muffin liner.
Break Brownie Brittle into small pieces, then place one piece on top of melted chocolate in each muffin tin. Place in freezer to cool while you make cookie dough.
In the bowl of a stand mixer fitted with paddle attachment, cream together butter, sugar, salt, and vanilla until very smooth, about 2-3 minutes. Add flour, then mix slowly until well combined. Fold in chocolate chips.
Remove cups from freezer, then place 1 tsp of cookie dough in each cup. If you have leftover melted chocolate, use that first, otherwise, melt second bag of chocolate chips according to directions above, then place enough melted chocolate on top to completely fill muffin liners. Sprinkle each with a pinch of maldon sea salt. Return to freezer for 2 hours, or until set.
To heat treat flour, line a baking sheet with parchment paper, then place flour on top. Preheat oven to 350 F and cook flour for 5 minutes. Remove from oven and let cool completely before continuing with recipe.