Preheat the oven to 350°F. Line an 8-inch-square baking pan with parchment paper, allowing it to overhang the edges. Coat the paper and pan sides with cooking spray. Set aside.
In a large bowl, whisk brown sugar and oil until combined.
Add eggs and vanilla and whisk until combined.
In a medium bowl, stir together the rye flour, all-purpose flour, baking powder and 1/2 teaspoon flaky salt.
Add the dry ingredients to the wet ingredients, stirring until just combined.
Fold in 3/4 cup chocolate chips.
Scrape the mixture into the prepared pan and sprinkle with the remaining 1/4 cup chocolate chips and 1/4 teaspoon flaky salt.
Bake until a toothpick inserted in the center comes out clean, 25 to 30 minutes.
Let cool in the pan on a wire rack for 1 hour before cutting into squares.
Notes
* You can make these ahead. Store at room temperature for 3 days or freeze for up to 3 months.