In a shallow bowl, whisk together the brown sugar and cinnamon until evenly combined. Set aside for coating the fried shells.

Using a 3.5 to 4-inch round cookie cutter, cut circles out of the flour tortillas. Heat about 1 inch of oil to 350°F in a large skillet or saucepan. Fry tortilla circles in batches for 10 to 15 seconds, flip, then fold into a taco shape and fry for another 15 to 20 seconds until golden brown and crispy. Remove and drain excess oil.

While the shells are still warm, coat them in the cinnamon sugar mixture, pressing the coating onto both sides. Place them over the bars of an upside-down muffin tin or wire rack to cool and hold their shape.

In a saucepan, whisk together water, brown sugar, cornstarch, cinnamon, and nutmeg. Cook over medium heat for 2 to 3 minutes until thickened and bubbling. Add diced apples and vanilla extract, then cook for about 10 minutes until apples are softened. Cool completely.

Beat softened cream cheese with an electric mixer until smooth. In a separate chilled bowl, beat cold heavy cream, powdered sugar, and vanilla extract until stiff peaks form. Fold whipped cream into the cream cheese mixture until smooth.

Transfer the cheesecake filling to a piping bag or zip-top bag with the corner cut off. Pipe the filling into each cooled cinnamon sugar shell and top with cooled apple pie filling.

Serve immediately for the best texture while the shells are still crispy.