Line a cookie sheet with parchment paper. Set aside.
In a small bowl, use a fork to mix together the ground flaxseed meal with the 2 ½ tablespoons of water. Set aside for 5 minutes, until it becomes a thick gel.
In a medium microwave-safe bowl add ⅔ (about 6 ounces) of the chocolate chips with 1 tablespoon of the vegan butter. Melt in the microwave for 30-second intervals, stirring in between, until fully melted.
In a bowl of an electric stand mixer fitted with a paddle attachment (or using a handheld mixer with a bowl), combine the remaining 5 tablespoons vegan butter, brown sugar, and granulated/cane sugar. Beat on medium speed 3 minutes, until combined and creamy.
Pour in the in melted chocolate mixture and mix. Then, add the flax mixture and mix until combined.
Add the almond flour, cocoa powder, baking soda and salt into the butter-flax mixture and mix on medium speed until a cookie dough texture forms.
Add ⅓ (roughly 3 ounces) of the remaining chocolate chips/chunks, and fold into the cookie dough.
Use a ¼ cup scoop or measuring cup to measuring 9 cookie dough balls and place onto the parchment-lined baking sheet, leaving 2 inches of space between each ball of dough. If making smaller cookies (totaling 18 cookies), scoop 2-tablespoonfuls per cookie.
Refrigerate or freeze the dough while you set the oven to preheat to 350°F.
Bake cookies for about 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!