Preheat the oven to 325°F (163°C). Line two large baking sheets with parchment paper and lightly spray with nonstick spray; set aside.
Place 1 cup of the chocolate chips and the coconut oil in a microwave-safe bowl. Heat on low power in 15-second increments, stirring between each, until completely melted and smooth; alternately melt in a small saucepan over low heat. Transfer to a large mixing bowl.
Whisk the granulated sugar into the melted chocolate, then whisk in the applesauce, almond milk, and vanilla until smooth.
In a medium bowl, whisk together the flour, cocoa powder, baking powder, and salt until evenly combined.
Add the dry ingredients to the wet ingredients and stir until just combined; do not overmix.
Fold in the remaining 1 cup of chocolate chips until evenly distributed.
Use a measuring scoop or a scant 1/4-cup measure to portion the batter onto the prepared baking sheets, leaving space for spreading.
Place one baking sheet in the oven and immediately reduce the oven temperature to 300°F (149°C). Bake for 20 minutes, then repeat with the second sheet if needed.
Allow the cookies to cool completely on the baking sheet before moving them; moving while hot will cause them to fall apart.