Preheat the oven to 350°F (180°C). Grease a 9 x 5-inch (23 x 13cm) loaf pan (or line it with parchment paper).
Brownies: In a medium bowl, combine the maple syrup, sugar, almond butter, milk, vanilla, baking soda, flax seed (if using), flour, cocoa, and salt, stirring to combine. Pour the brownie batter into the loaf pan. Sprinkle the top of the batter with the chocolate chips. Bake for 11 to 13 minutes, or until the center is set.
Cheesecake: In another medium bowl, combine the yogurt, almond butter, vanilla, lime juice, cornstarch, salt, and sugar. Taste and add more lime juice and sugar if needed (keep in mind that the lime juice will taste stronger after baking).
Take the brownies out of the oven and pour the cheesecake mixture over the brownies. Sprinkle the top of the cheesecake with the chocolate chips. Bake for 25 minutes, or until the center of the cheesecake is set. Cool completely and chill for at least 30 minutes. Slice and serve.