Preheat the oven to 350°. Grease and line a 9x9 inch square pan with parchment paper. Set aside.
In a large bowl mix all of the shortbread ingredients: almond flour, coconut flour, maple syrup, melted coconut oil, maple syrup, vanilla and salt.
Reserve ¼ of the mixture for the crumble topping. Take the remaining mixture and gently press it down in the lined square pan. Bake for 12-14 minutes, or until lightly brown around the edges. Once the crust is fully cooked, remove from the oven and set aside.
While the shortbread is cooling start the apple layer. Dice the 2 large apples into small cubes and transfer to a large bowl. Add the remaining maple syrup, melted coconut oil, arrowroot powder, cinnamon, salt, vanilla, and lemon juice. Stir the mixture until the apples are evenly coated.
Pour the apple mixture into a large saucepan and add 2 tablespoons of water. Cook on medium heat, while continuing to stir, until sauce begins to thicken. Apples will begin to caramelize at about 5-7 minutes.
Once the apples have caramelized turn off the heat and carefully pour the apple mixture over the top of the shortbread crust, spreading evenly.
Take the reserved shortbread dough and toss in the chopped pecans and cinnamon, creating a crumb-like mixture. Sprinkle the crumble topping evenly over the caramelized apples, then gently press down with a fork to secure.
Return the pan to oven and bake for 20-25 minutes, or until the crumble topping is golden brown.
Remove the pan from the oven and allow the bars to cool for 30 minutes. Then transfer the bars to the refrigerator for at least 4 hours, (or overnight).
Cut the bars into 16 squares, serve immediately.
Bars can be kept in the refrigerator for up to 5 days.