Grease a 9x11 inch pan and set aside. Preheat the oven to 350 degrees.
In a bowl set over a saucepan of simmering water, melt the chocolate with the butter, stirring a few times, until smooth, about 7 minutes.
In a small bowl, sift together the flour and baking powder. Set aside
In another large bowl, using a handheld electric mixer beat the eggs with the sugar at medium speed until thick and pale, about 5 minutes. Beat in the vanilla and salt.
Add the apple sauce to the melted chocolate and mix to combine.
Using a rubber spatula, fold the chocolate mixture into the egg mixture a little at a time, then fold in the flour and baking powder mixture.
Stir in the chocolate chips.
Scrape the brownie batter into the prepared pan, then smooth it into an even layer.
Bake for 25 minutes, until the edges are set and the center is slightly firm..
While the brownie base is baking, make the pecan pie topping.
In a medium-sized bowl, cream together the butter and brown sugar. Add the maple syrup, corn syrup, salt, whiskey (or vanilla) and beat until combined. Add the eggs, one at a time, and mix until combined. Stir in the pecans.
After 15 minutes, remove the brownies from the oven and gently pour the pecan mixture on top, and spread until even in a thin layer.
Return to the oven and continue baking for another 40-45 minutes until the pecans and center of the brownies are set.
Turn off the oven and leave the brownies inside for 10 minutes. Remove and place on a cooling rack.
Allow to cool completely (for at least 30 minutes) before cutting.