Whisk together flour and baking soda; set aside.
Combine coconut sugar, melted coconut oil, egg, egg yolk, salt and vanilla, whisk until mixture is smooth and no lumps remain, 30 seconds. Let mixture stand for 3 minutes then whisk vigorously for 30 seconds and rest for 3 minutes. Repeat process of whisking and resting 2 more times, ending with resting, until mixture is thick, fluffy, smooth and shiny. Whisk in almond butter and beat until thick, 1 minute.
Using a rubber spatula, stir in flour mixture (reserve ½ teaspoon flour to toss with chocolate chips) until nearly combined. Toss chocolate chips with reserved ½ teaspoon flour to coat; add chocolate chips to dough and mix just to combine.
Working with 3 tablespoons (#20 scoop) dough at a time, roll into balls and space 2 inches apart on prepared sheets.
Chill sheets with dough balls for at least 30 minutes.
Meanwhile, heat oven to 375ºF with rack set in middle position.
Bake 1 sheet at a time until cookies are golden brown, puffy, and edges have begun to set but centers are still soft, 12–14 minutes, rotating sheet halfway through baking. Transfer sheet to a wire rack, sprinkle cookies with sea salt, and cool completely.
Store cookies in an airtight container at room temperature for up to 5 days (best within 3 days).