In a small bowl, combine flax, water and vanilla. Stir and set aside.
In a large bowl using a wooden spoon or in the bowl of your stand mixer fitted with the paddle attachment combine the earth balance, sugar and molasses until creamed, scraping the bowl down a couple of times to ensure everything combines evenly.
Add flax mixture and combine well.
Add gluten free flour, salt, cinnamon and xanthan. Stir until well combined.
Add the oats and baking soda and stir until combined.
Add chocolate chips and stir once more until evenly distributed.
Leave cookie dough on the counter to rest for 1 hour.
Preheat oven to 350* F. Line a cookie sheet with parchment.
Scoop dough in about 2 tablespoon mounds leaving 2 inches of space between each cookie. Give the mounds a gentle press down so they are less of a mound and more of a disc.
Sprinkle the tops of the cookies with a sprinkle of coarse sea salt.
Bake in a 350* oven for 13-16 minutes or until the edges are brown and set. Let cool on the cookie sheet for 10 minutes before transferring to a cooling rack.