Line 2 rimmed sheet pans with parchment paper or silicone baking mats. Set aside.
In the bowl of an electric mixer fitted with the paddle attachment, cream the butter on high speed, about 30 seconds. Add the sweetener and beat until light, fluffy, and thoroughly mixed, scraping bowl a few times, about 2 minutes.
Add the almond butter and beat until well combined. Add the egg and vanilla and mix until just combined.
In a separate bowl, combine the almond flour, coconut flour, baking soda, and salt. Use a whisk to mix well and break up any lumps. With the mixer on lowest speed, slowly add dry ingredients to the wet mixture and beat on low speed until just combined. Use a rubber spatula to fold in the chocolate chips. Cover the dough and refrigerate for 1 hour.
Preheat the oven to 350°F (180°C). Using a portion scoop or a tablespoon to measure out 3/4-ounce (1-1/2 tablespoon) portion balls. Place the dough balls onto the prepared baking sheet pans, 10 on each pan, about 2 inches apart. Freeze for 15 minutes.
Place the cookies direct from freezer into oven, bake for 6 minutes, then press down gently on each cookie with the back of a spoon to flatten to a uniform shape. Return to the oven and bake until the cookies just begin to brown around the edges, 6 to 8 minutes more.
Remove the cookies from the oven, sprinkle with flaky sea salt, and let cool completely on the pans for 1 hour.