Prepare a 10-inch springform pan with a lining of parchment paper.
Make The Crust:
Pulse the pecans and almond flour together in a food processor until the mixture is fine. If you don't have a food processor, finely chop the pecans and mix them with the almond flour in a bowl.
Transfer the pecan mixture to a mixing bowl. Add the melted butter, brown sugar substitute, granulated sugar substitute, and cinnamon. Stir or mix with your hands until the mixture resembles wet sand.
Use your hands to press the crust mixture evenly into the bottom of the prepared springform pan. Use the back of a spoon and compact the crust, especially around the edges.
Place the pan with the crust into the freezer to chill and set while you prepare the filling.
Make The Cheesecake Filling:
In a large mixing bowl, beat the heavy cream with a hand mixer until stiff peaks form, about 1-2 minutes.
In a separate bowl, beat the softened cream cheese and vanilla extract until smooth. Gradually add the powdered sugar substitute, beating until fully combined and fluffy, about 1 minute.
Gently fold the cream cheese mixture into the whipped cream with a spatula until combined, about 30 seconds.
Place the dark chocolate chips in a heatproof bowl over a pan of gently simmering water. Stir constantly over medium-low heat until melted, then remove from heat. Let cool for about 10 minutes, until room temperature but still fluid. Alternatively, melt the chocolate in the microwave in 15-second intervals, stirring between each, until melted.
Remove 1 cup of cheesecake filling and stir it into the cooled, melted dark chocolate until thoroughly combined.
Remove the crust from the freezer. Spread the chocolate cheesecake mixture evenly over the crust and smooth the top.
Stir the chopped pecans into 1/4 cup of the caramel sauce. Spoon this mixture over the chocolate cheesecake layer.
Spread the remaining plain cheesecake filling over the caramel pecan layer. Smooth the top with a spatula.
Chill The Cheesecake:
Refrigerate the assembled cheesecake for 6 to 8 hours, or until fully set. For the cleanest slices, move the cake to the freezer for about the last 30-60 minutes, but monitor it closely so it doesn’t freeze solid.
Make The Chocolate Ganache:
Heat the heavy cream in a saucepan until hot but not boiling. Remove from heat. Add the chocolate chips and butter. Let sit undisturbed for 4-5 minutes to soften, then stir with a balloon whisk or fork until smooth.
Finish And Serve The Cake:
Remove cheesecake from fridge or freezer and allow it to return to just below room temperature. Run a thin knife around the edge to loosen the cake, release the sides of the springform pan, then transfer the cake—still on the pan base and parchment—to a platter or serving dish.
Using a spoon or a clear piping bag with a very small tip, drizzle the ganache over the cheesecake. If the ganache is too thick, briefly reheat for easier drizzling. Optionally drizzle 1-2 tablespoons of the caramel sauce over the cheesecake, as well.