For the brownies:
Preheat the oven to 325°F. Line an 8×8-inch pan with foil, leaving an overhang.
In a large bowl combine the butter, sugar, cocoa powder, and salt. Stir until well combined, mixture will be thick. Let cool if the butter is still hot. Stir in the vanilla and then the eggs, one at a time, stirring very well after each addition. Stir until the batter is very well blended. Add the flour and stir again until very well blended. Spread into prepared pan.
Bake for 15 minutes, or until just starting to set but not fully cooked. Let cool to room temperature then place in the fridge to chill until ready to use. Maintain 325°F oven temperature if baking cheesecake layer immediately.
For the cookie dough:
In a large bowl, use an electric mixer to beat the butter, brown sugar, granulated sugar, salt, vanilla, and milk until smooth, about 2 minutes. On low speed gradually add the flour and beat until combined. Mix in the chocolate chips. Set aside.
For the cheesecake:
In a large bowl, use an electric mixer to beat the cream cheese and sugar until well combined and smooth. Beat in the eggs, flour, and salt just until incorporated. Pour the cheesecake batter over the brownie. Scoop out balls of cookie dough and flatten with your hands before placing over the cheesecake batter to cover all the batter.
Bake at 325°F for about 50 minutes, or until the cheesecake is set and the cookie dough is barely golden but dry. Cool to room temperature before refrigerating for at least 2 hours to chill. Cut into 12 bars before serving. Bars can be stored in an airtight container in the fridge for up to 3 days.