Preheat oven to 350 degrees F. and grease or line a cupcake pan.
Wrap beet roots in aluminum foil and bake for about 45 minutes or until beets are soft enough for a knife to slide easily through. Let cool, then peel.
In a food processor, pulse beets. Add sour milk and blend until smooth.
In a large bowl, sift together flour, cornstarch and cocoa powder. Set aside.
In a separate bowl, whisk together sugar, eggs, oil and vanilla.
Alternate adding flour mixture and beet puree to the wet ingredients. Fold each addition with a spatula, beginning and ending with the flour mixture, until you have a smooth batter.
Fill each cupcake pan and bake for about 20 minutes or until the cake tester comes out clean.
Remove the cupcakes and transfer to a cooling rack. Let cool completely.
In the bowl of your standmixer with the whisk attachment, beat cream cheese until smooth. Add sugar, ¼ cup at a time. Add evaporated milk one tablespoon at a time until a smooth, thick frosting comes together. Top each cupcake with frosting.
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