Step 1Heat the oven to 350 degrees. Butter a 13-inch by 9-inch baking pan and line with parchment paper.
Step 2In a heatproof bowl, melt together the butter and chocolate over a pan of water that has been brought to a boil and then taken off heat. Set the mixture aside to rest, stirring occasionally as it melts.
Step 3In a separate bowl, whisk together the cocoa, rye flour, baking powder and salt.
Step 4In the bowl of a stand mixer, beat together the sugars, eggs and vanilla until light and fluffy. Slowly add the melted chocolate, followed by the dry ingredients. Mix just enough to combine, then spread into the prepared pan, smoothing the top with a spatula. Sprinkle the sea salt flakes over the batter.
Step 5Bake until the brownies are set but with a slight wobble, 20 to 25 minutes. Cool completely in the pan before cutting into bars. These are best eaten the day of baking.