Preheat oven to 350. Line a 9 inch square pan with a strip of 9 x 14″ wax paper. (If it falls down, use metal clips to keep it in place). In a large bowl, mix together the almond flour, sugar, salt, and vanilla. Add the melted butter and mix until well combined. Press mixture into the pan and bake for 15-20 minutes, just until the edges barely begin to brown. Remove from oven and let cool.
Filling:
Reduce heat to 325. Using an electric mixer, beat together the cream cheese, sugars, and salt. Add the eggs one at a time, then the vanilla extract. Add the heavy cream and flour and mix until just incorporated. Fold in the pecans and pour filling over cooled crust.
Take a roasting pan large enough to hold the baking dish. Place a wet dish towel on the bottom of the roasting pan, then add the baking dish. Fill the roasting pan halfway with water. Bake for about 30 minutes, until the middle barely jiggles. Turn the oven off and keep the door partially open. Let the cheesecake sit in there for 1-2 hours to allow it to set. Move to the refrigerator for a minimum 2 hours, or overnight. Do not cover until it’s completely cool. (For cleaner slices, put in freezer prior to cutting)
Topping:
In a small saucepan, whisk together the cream, brown sugar, and salt over medium heat. Bring it to a boil, and let it remain at a boil for about 1 minute. Remove from the heat and add in the vanilla and powdered sugar. Keep mixing until most of the lumps from the sugar are gone. Mix in the pecans. Let it cool slightly while you cut the squares.
Remove the cheesecake from the fridge or freezer and remove it using the wax paper. Use a warm sharp knife to cut into 16 slices. Clean the knife after each slice. Top with pecan halves and drizzle topping over the squares. Place immediately back into the fridge or freezer to let the topping cool completely.