Preheat the oven to 350 degrees. Line a large cookie sheet with parchment paper.
In a small bowl, whisk together the ground flaxseed and filtered water. Let stand for 5 minutes to thicken.
Using a stand mixer fitted with the paddle attached (or electric beaters), beat the melted coconut oil, coconut sugar, and maple syrup on medium-high for 30 seconds, or until it forms oily mounds. Add the vanilla and the flaxseed mixture. Beat on medium until just incorporated (10 to 15 seconds).
Add the spelt flour, arrowroot, baking soda, and sea salt. Mix on low to medium-low for 10 to 15 seconds, or until incorporated and the mixture just begins to pull together into large mounds of dough as it moves around the bowl. Do not over-mix (spelt's gluten structure is delicate and over-mixing can result in tough, dry, or crumbly cookies).
Use your hands to press the crumbles together into a dough. Add the chocolate chips and incorporate with your hands or use a spoon to stir the chips into the dough.
Roll the dough into 12 to 14 large balls ( about 2 tablespoons each) or use a cookie scoop to scoop out tightly packed mounds of dough. Place on a cookie sheet (press any loose chocolate chips into the top of the dough).
Bake for 7 to 10 minutes, or until the cookies look puffy, dry and just barely light golden on top (I bake mine for 8 minutes). Do not over-bake (or your cookies will lose their soft, chewy quality). In fact, if in doubt, err on the side of under-baking.
Let the cookies cool for 5 minutes on the pan. Then, use a metal spatula to carefully transfer them to a cooling rack and cool completely (about 30 minutes). They will fall just a touch as they cool.
Store in an airtight container for up to 4 days, refrigerate for up to 1 week, or freeze for up to 1 month.