In a large bowl, add the almond flour, flaxseed, maple syrup, 1/4 cup (4 tablespoons) of the coconut oil, vanilla extract, and a pinch of salt. Mix until well combined.
Fold in 2/3 cup of the chocolate chips.
Spread the mixture into a thin, even layer on the lined baking sheet. Note that using your hands may work best - the mixture will be sticky!
In another bowl, add the remaining chocolate chips and 1 tablespoon of coconut oil. Microwave on high for 2 minutes, stirring halfway through. Using a spoon, mix the melted chocolate until smooth.
Pour the chocolate on top of the cookie dough evenly, smoothing it out with a spoon or spatula. Top with flaky salt.
Place in the freezer to harden for at least an hour, and then cut into squares.