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In a small saucepan over med-low heat, cook apples, brown sugar, cinnamon, and vanilla together, about 5 minutes. Once the apples have softened, take the mixture off the heat and allow to cool to room temperature, about 5-10 minutes.
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Pour cake mix into a large bowl, and mix with canola oil and eggs. Add in apple mixture, and mix until combined. Batter will be thick.
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Chill in the fridge for 15-20 minutes.
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Preheat oven to 350 degrees.
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Drop cookies by rounded Tablespoons onto a cookie sheet lined with parchment paper (for a smooth cookie surface when baked, make sure the cookie dough balls are smooth on top before placing in the oven).
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Bake for about 10 minutes, or until cookies look set (barely golden brown, and do not look doughy in the centers). Whoopie pies are traditionally a soft-baked cookie with a cake-like texture, thus you don't want to over bake them.
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Allow cookies to cool completely.
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Cream butter and cream cheese together, until well combined, about 1-2 minutes. Add in vanilla and cinnamon. Mix. Add in powdered sugar, and mix until well combined.
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With a spoon or a piping bag with a circular tip, add about 1 Tbsp (more or less, depending upon your preference) of filling to half of the cookies. Top with the other halves.
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Enjoy!
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For best results, store leftovers in the fridge.