Preheat oven to 350 F, line a baking sheet with parchment paper.
Cut marshmallows in half, set aside. Drain cherries, remove stems and dab off extra moisture with a paper towel. Cut cherries in half, set aside.
Mix the flax meal with water and set aside for 5 minutes, until thickened.
In a stand mixer cream butter and sugar together. Add flour, baking soda, cocoa and salt until well combined. Add the milk, vanilla and flax egg to the creamed mixture, combine. A sticky and thick dough will form, do not overmix.
Scoop dough out 1 leveled tablespoon at a time and roll into balls, place on baking sheet with 2 inches between cookies. If you have a small cookie scoop you can skip rolling into balls and just lay flat side on parchment. Bake 5 minutes, add marshmallow half, sticking it into the top of the cookie and bake 4 more minutes until the marshmallow puffs up just slightly. Remove from oven, transfer to a cooling rack and let cool completely.
Melt chocolate chips in microwave or double boiler. Dip the top of each cookie in chocolate to coat the marshmallow. Top each marshmallows with a cherry.
Let sit for 1 hour for the chocolate to set, transfer to the refrigerator to speed the process up if need be.