In a small bowl, mix together the flax and water and let sit until slightly thickened (about 5-7 minutes).
In the bowl of a stand mixer, cream together the butter and sugars until light and fluffy, about 5 minutes. Add the flax and vanilla and mix for another 2 minutes until fully combined.
Sift together the dry ingredients (flour, baking soda, and salt) and add into the mixing bowl all at once. Mix on low until the flour is just incorporated.
Fold in the chocolate chips and granola.
Add spoonfuls of the almond butter to the top of the dough, then fold together with a spatula just until the almond butter is starting to incorporate into the dough. You can also do this with your stand mixer: just quickly turn the mixer on and off a few times and you'll achieve the same result.
Scoop the dough onto a parchment-lined baking sheet, cover with plastic wrap, then chill in the fridge at least 2 hours, overnight if possible. When you're almost ready to bake the cookies, preheat the oven to 350º.
Bake 15-17 minutes until golden brown around the edges.