Sift together flour, cocoa powder, baking powder, and baking soda. Set aside.
In the bowl of an electric mixer fitted with the paddle attachment beat butter, vegetable shortening, granulated sugar, and 1 cup light brown sugar on medium speed until light and fluffy, about 2 minutes. Add eggs, 1 at a time, mixing until fully combined between each addition. Add vanilla beat to combine. Gradually add dry ingredients and mix on low speed until fully combined. Remove from mixer. Using a wooden spoon, stir in chocolate chips. Cover bowl with plastic wrap and chill until firm, about 1 hour.
Heat oven to 350 degrees F.
Line baking sheets with silpats (French nonstick baking mats) or parchment paper.
In a small bowl using a rubber spatula, stir together peanut butter and remaining 1/4 cup light brown sugar.
Using a 1 1/4-inch scoop or heaping tablespoon, drop dough onto prepared baking sheets about 2 inches apart. Make a thumbprint in the center of each cookie. Fill thumbprint with 1 teaspoon peanut butter mixture. Top with a second scoop of dough and carefully mold dough to cover "surprise".
Bake until firm, about 12 minutes. Transfer to a wire rack to cool for 5 minutes before transferring cookies to wire rack to cool. Repeat with remaining dough.
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