Line an 8x8-inch square pan with parchment, leaving an overhang for easy removal later and set aside.
Make the cookie dough: In a medium bowl, whisk together the almond flour, vanilla protein powder and fine sea salt until evenly combined.
Add the almond butter, maple syrup, almond milk and vanilla extract. Use a silicone spatula to fold and press the mixture until it comes together into a soft, slightly sticky dough. If it feels too dry, add 1/2 teaspoon more milk; if too wet, sprinkle a little more almond flour.
Fold in 1/4 cup mini chocolate chips, then transfer the dough to the prepared pan. Press the dough into an even layer about 1/4- to 1/2-inch thick, using a piece of parchment or the back of a spoon to smooth the surface.
Firm the base: Freeze or refrigerate the pan for 10 minutes so the dough becomes firmer and easier to top without mixing into the melted chocolate.
While the dough chills, melt the chocolate: Place the chopped dark chocolate and coconut oil in a heatproof bowl. Microwave in 20–30 second bursts, stirring between each, until fully melted and glossy. Alternatively, melt over a double boiler and stir until smooth.
Pour the melted chocolate over the chilled cookie dough, using an offset spatula to spread an even layer. Work quickly so the chocolate doesn’t set before it’s smoothed.
Immediately sprinkle the remaining mini chips over the warm chocolate and finish with flaky sea salt flakes. Gently press any loose chips into the chocolate so they adhere as it sets.
Set the bark: Return the pan to the refrigerator for at least 20 minutes (or the freezer for 10–15 minutes) until the chocolate is firm and the bark is solid.
Remove from the pan using the parchment overhang and break into 10 irregular pieces. Store in an airtight container in the fridge for up to 2 weeks or freeze for longer keeping.