Preheat the oven to 350ºF and line a cookie sheet with parchment paper.
In a bowl or stand mixer, beat together the coconut oil, nut butter, and coconut sugar until smooth. Add the flax eggs and vanilla and mix until smooth.
Add the baking soda, salt, coconut flour, and rolled oats to the wet ingredients. Mix until well incorporated. Fold in the chopped dark chocolate.
Use a cookie scoop to form cookies and place 2” apart on the prepared baking sheet. Press down slightly to flatten - note that the cookies won’t spread very much, so press them down to the thickness you prefer. Sprinkle with a bit of flaky sea salt if desired. Bake for 10 minutes or golden brown around the edges.