In a small bowl, combine ground flax, instant espresso powder, vanilla and water. Stir to combine and set aside.
In a large bowl using a wooden spoon, or in the bowl of your stand mixer fitted with the paddle attachment, cream the butter, sugar and molasses together until creamy and well combined.
Add the flax mixture and mix well.
Add the cocoa powder and mix until well combined.
Add flour, salt, baking powder and baking soda and mix until just combined.
Add chocolate chips and mix just until they are distributed.
Cover and place the dough in the refrigerator for 1 hour to chill.
Preheat oven to 350* F. Line a sheet tray with parchment.
Using a ¼ cup measure that has bee sprayed with nonstick spray, portion out the dough into 14 mounds.
Working one at a time, make a well in a mound of dough and place 3-4 mini marshmallows into the well. Then, cover the marshmallows and gently roll the dough into a sphere with the palms of your hands.
Repeat until all the cookies are stuffed with marshmallow.
Place 6-8 dough balls on a cookie sheet, leaving at least 2 inches of space between each. Place the remaining dough balls back into the refrigerator.
Gently press the balls down to keep them from rolling around. Sprinkle each cookie with flakey sea salt, then bake in a 350* oven for 18-21 minutes or until the edges of the cookies are set.
Allow the cookies to cool on the baking sheet for at east 5 minutes before moving to a wire cooling rack to cool completely.
Repeat with the remaining cookie dough balls.
Cool slightly, serve.