Place the chocolate chips in the freezer. Then, start by heat treating the flour to kill any bacteria. Add the flour to a parchment lined baking sheet and distribute evenly. Preheat the oven to 350℉/177℃ then bake for 8 minutes and allow to cool completely. Once cool, sift into a bowl to remove any clumps that formed during baking.
Cream together the butter and sugars on medium high speed for about three minutes until fluffy. Add the vanilla and peanut butter, mix to combine, then scrape down the sides.
With the mixer running on low speed, add the salt and sifted flour to the dough. Once all flour has been incorporated, add in the sweetened condensed milk in a steady stream with the mixer still running on low.
Scrape down the sides once more, then add the cold chocolate chips and mix on the lowest setting until evenly dispersed.
Prepare an 8x8 inch baking pan with parchment paper slings, then add the dough to the pan. Using a spatula, bottom of a measuring cup, or clean fingers, press the dough evenly across the pan, being sure to get the dough the whole way into the sides and corners.
Place in the fridge to set for about an hour.
To make the topping, add the peanut butter and chocolate to a bowl and microwave in 20 second increments, stirring after every 20 seconds, until completely smooth. You could also do this in a double boiler. Pour over the chilled cookie dough and spread evenly.
Chill until the chocolate layer is set, top with flaky salt, then slice into 36 squares.