Prepare two baking sheets with parchment paper and set aside.
In a medium-sized bowl, whisk together the flours, baking powder, baking soda, and salt. Set aside.
In a large bowl, use a hand mixer or stand mixerwith a paddle attachment to cream the butter, about 30-45 seconds. Add in the sugar and continue to cream the butter mixture for about 1-2 minutes. The mixture should look a pale yellow.
Gradually add in the flour mixture to the butter mixture. The mixture will be a bit crumbly, so don't worry if it looks off. Add in eggs and mix until fully combined. Place dough in the refrigerator while you make the apple filling and crumbs.
Make the apple filling. In a small saucepan, combine the chopped apples, nutmeg, cinnamon, and water on low heat. Cook the apples for about 10 minutes or until they start to go soft. You don't want them to be too mushy because they will cook again in the oven. When a fork can go through them easily, they are done.
Remove the filling from the heat and let cool. Make the crumb topping while the filling is cooling.
Add the flour, brown sugar, cinnamon, and melted butter in a small bowl. Mix with a fork until crumbs start to form. The crumbs should be about the size of a pea. Feel free to add in more/less cinnamon and adjust to your taste.
Take the dough out of the fridge and fold in about 3/4 of the crumbs. If the crumbs are difficult to fold in, let the dough sit for a minute to warm up. The dough will be a little lumpy, but don't worry if it does not incorporate fully.
Make the cookie dough balls. Each ball should weigh around 6 oz or 3/4 cups. The dough should make around 5-7 large cookies. Once the dough is in a ball, take about a quarter chunk of dough off the top and flatten it to form a round disc. Flatten the dough with your thumb to form a well. Inside the well, place a heaping tablespoon of the filling and a small sprinkle of the crumbs. The filling should completely fill in the well. Cover the well and filling area with the remaining cookie dough. Repeat for the remaining cookies.
Sprinkle additional crumbs on top of the cookie and place them the freezer to chill for 90 minutes.
When the cookies are almost ready in the freezer, preheat the oven to 375°. In order to get a solid cook, place one empty baking sheet upside-down in the oven and place the tray with the cookie dough on top of it. Bake for 24-26 minutes, or until the edges show a golden brown tint.
Let the cookies come to room temperature before enjoying! Store the cookies in an air-tight container.