When working with frozen phyllo sheets, remove just the number of sheets that you need to prepare recipe. Re-roll remaining phyllo sheets, wrap tightly in plastic wrap and refrigerate up to 1 week or refreeze for up to 3 months.
Phyllo cups can be prepared ahead of time. Store cooled cups in tightly covered container at room temperature up to 3 days. Pudding and apple mixture can also be prepared ahead of time and stored in separate tightly covered containers in refrigerator until ready to spoon into phyllo cups as directed. Filled phyllo cups can be stored in refrigerator up to 2 hours before serving.
Omit whipped topping. Garnish each filled cup with 1/2 tsp. sifted icing sugar and 1 tsp. toasted chopped pecans.