Preheat oven to 350°F and line a cookie pan with parchment paper.
Combine 1 cup chocolate chips and 1/4 cup plant-based milk in a microwave safe bowl, stir together, and then heat in the microwave for 30 seconds. Stir the two together. Heat again in 10 - 15 second increments, until the chocolate chips are melted and the mixture is smooth. Set aside to cool slightly.
Combine the softened vegan butter and sugar in a mixing bowl and beat with a mixer until light and fluffy.
Add the ground flax, cornstarch, water, vanilla, and apple cider vinegar. Use the mixer and beat until combined.
Add the melted chocolate mixture and beat on high, until fluffy.
In a separate bowl whisk together the flour, cocoa, baking soda, baking powder, and salt. Pour this to the chocolate butter mixture and beat until well combined. Add the remaining 1 cup of chocolate chips and stir until equally distributed throughout the batter.
Use a cookie scoop to evenly distribute cookie dough onto a cookie sheet. Bake for 9 - 11 minutes, until the cookies are done. Remove the pan from the oven. Allow cookies to cool 1 - 2 minutes on the pan before transferring to a wire rack to cool completely. Repeat until all the cookies are made and cooled.