Preheat the oven to 350°F (175°C) and line two baking sheets with parchment paper. Set aside.
In a small bowl, stir together the flax meal and water and then set it aside to gel for about 5 minutes.
In a large bowl using an electric mixer, beat the butter until light and fluffy, 1 to 2 minutes. Then add the brown and white sugar and continue beating until smooth and creamy, about 1 minute. Add the flax mixture and beat to combine. Set aside.
In another large mixing bowl, stir together the flour, baking powder, and baking soda and add half of it to the butter mixture and mix until combined. Add the remaining dry ingredients and mix until combined, about 30 seconds. Add the chocolate and mix until incorporated and evenly distributed. Scoop balls of dough, about 2 tablespoon (50-55g) of dough for each cookie, and place them 2 to 3-inches (5-7.5cm) apart on the prepared baking sheets.
Bake one baking sheet at a time for 8 minutes and then remove it from the oven and tap the baking sheet against the counter 1-2 times to deflate the cookies. Then bake them for 1-2 minutes and deflate the cookies again. Continue baking for 1-2 minutes or until the edges start to lightly brown.
Let them cool on the baking sheets for 5 minutes before carefully transferring them to a cooling rack to continue cooling. Sprinkle with flaky sea salt before serving. Store them in an airtight container at room temperature for up to 4 days or freeze for up to 3 months.