Combine sugar, cocoa and flour in a medium saucepan. Add milk and butter. Bring to a boil, stirring constantly. Remove from heat. Stir a small amount of the hot filling into the beaten eggs. Return all of the egg mixture back to the saucepan, whisking constantly to incorporate. Fold in half of the cherry pie filling and the chocolate chips. Pour filling into the pie shell and bake for 35-40 minutes or until set. Cool and refrigerate for at least one hour.
Spoon whipped topping over pie then artfully arrange the remaining cherry pie filling on top.