Preheat the oven to 350°F and line a baking sheet with parchment paper. Set aside.
To prepare the “flax egg” mix together a ground flaxseed meal with the 2 ½ tablespoon water in a small bowl. Set aside for 5 minutes, until it becomes a thick gel.
In a microwave-safe bowl, melt ⅔ (roughly 6 ounces) of the semi-sweet chocolate at 30-second intervals, stirring in between, until melted. Be sure to save the remaining 3 ounces of chocolate for later! If you’re nervous the chocolate will burn, add 1 tablespoon of the vegan butter to the chocolate to help with melting easily.
In a bowl of an electric stand mixer fitted with a paddle attachment (or using a handheld mixer with a bowl), combine the vegan butter, brown sugar, and granulated/cane sugar. Beat on medium speed 3-5 minutes, until combined and creamy. Mix in melted chocolate mixture.
Next, mix the flax egg into the butter mixture just until combined.
Pour the almond flour, cocoa powder, baking soda and salt into the butter-egg mixture and mix on medium speed just until combined.
Chop ⅓ (roughly 3 ounces) of the chocolate bar into small pieces and fold into the cookie batter.
Using a ¼ cup, scoop about 9 cookie dough balls onto the parchment-lined baking sheet, leaving 2 inches of space between each mound of dough. If making smaller cookies (totaling 18 cookies), scoop 2-tablespoonfuls per cookie.
Refrigerate or freeze the dough for 15 minutes (if you have the time).
Bake cookies for 18-20 minutes in the middle oven rack. Sprinkle cookies with flakey sea salt right after baking.
Allow cookies to cool on a wire baking rack for 10 minutes. Enjoy!