Preheat oven to 350°F Lightly spray bottom and sides of 9-inch spring form pan with no-stick cooking spray; set aside.
For crust, in small bowl combine graham cracker crumbs, sugar, cinnamon, nutmeg and butter. Mix well. Press crumb mixture firmly into bottom, and up the sides of the pan.
Bake 6 to 8 minutes. Remove; pour 1/2 cup caramel topping over the bottom of the warm crust. Sprinkle 1/2 cup pecan chips on top.
For cake, in large bowl, beat cream cheese, 1 tablespoon flour, and sugar; mix until smooth. Add eggs; mix well.
In small bowl combine apples, remaining flour and cinnamon; mix well. Fold apple mixture into cheese mixture; pour into prepared crust. Bake 45 minutes. Pour remaining caramel topping on cheesecake; bake 10 to 15 minutes or until cheesecake is set.
Remove to cooling rack; sprinkle remaining pecan chips over top. Cool to room temperature; chill in refrigerator overnight.