For the Cookies:
1 ounce semisweet chocolate, chopped
1/2 ounce milk chocolate, chopped
12 tablespoons unsalted butter, melted
1/2 cup sour cream
2 large eggs
1 1/2 teaspoons apple cider vinegar
1/2 teaspoon vanilla extract
1 tablespoon red food coloring
2 1/4 cups all-purpose flour
1 cup granulated sugar
1/4 cup unsweetened cocoa powder
2 teaspoons baking powder
1/4 teaspoon baking soda
1/2 teaspoon salt
For the Filling:
8 ounces cream cheese, at room temperature
3 tablespoons unsalted butter, at room temperature
2 1/2 cups confectioners' sugar, sifted
1 vanilla bean, halved lengthwise and seeds scraped
Make the cookies: Preheat the oven to 375 degrees F. Line 2 large baking sheets with parchment paper. Combine the semisweet and milk chocolate in a microwave-safe bowl and microwave at 50 percent power until melted, about 2 minutes. Whisk until smooth.
Whisk the melted butter, sour cream, eggs, vinegar, vanilla and food coloring in a bowl until combined. In another bowl, whisk the flour, sugar, cocoa powder, baking powder, baking soda and salt.
Add the flour mixture to the butter mixture in four equal batches, whisking each batch completely before adding the next. Stir in the melted chocolate.
Scoop heaping tablespoonfuls of batter onto the prepared baking sheets and smooth the tops with a damp finger. Bake until the cookies spring back when lightly pressed, 8 to 10 minutes. Let cool 10 minutes on the baking sheets, then transfer to racks to cool completely.
Meanwhile, make the filling: Beat the cream cheese and butter with a mixer until smooth. Beat in the confectioners' sugar and vanilla seeds. Sandwich a heaping tablespoonful of filling between 2 cookies; repeat with the remaining cookies and filling. Refrigerate 30 minutes before serving.