Instructions

for the filling

Using stand mixer fitted with paddle, beat all ingredients on low speed until sugar is mostly moistened, about 1 minute. Increase speed to medium-high and beat until fluffy and smooth, 2 to 3 minutes, scraping down bowl as needed.
Line rimmed baking sheet or large, flat plate with parchment paper. Using tablespoon measure and small spoon (or #60 scoop), divide filling into 12 equal portions on prepared plate. Use back of spoon to lightly flatten each portion into rough disk shape (no greater than 1½ inches in diameter). Freeze until solid, at least 2 hours. (Filling can be frozen for up to 1 week.)

for the cookies

Adjust oven rack to middle position and heat oven to 425 degrees. Line 2 rimmed baking sheets with parchment paper. Whisk all-purpose flour, whole-wheat flour, cocoa, salt, and baking soda together in large bowl.
Whisk melted butter, brown sugar, and granulated sugar in second large bowl until smooth. Whisk in eggs, lemon zest, vanilla, and food coloring until smooth and creamy, about 30 seconds. Stir in half of flour mixture with rubber spatula or wooden spoon. Stir in chocolate chips, pecans, and remaining flour mixture. (Mixture will be stiff; once dough begins to stiffen, you can mix with your hands until dough is evenly combined.)
Divide dough into 12 equal portions (about 3½ ounces; 99 grams; or ⅓ cup each). Flatten each dough portion into disk shape, about 3 inches in diameter. Working quickly, place 1 disk of frozen filling in center of each dough disk. Wrap edges of dough up and around filling, seal dough, and shape into smooth disk shape (about 3½ inches in diameter and ½ inch thick), taking care to ensure filling remains in center of each cookie. Space cookies evenly on prepared sheets, 6 cookies per sheet.
Bake cookies, 1 sheet at a time, until edges of cookies are beginning to puff and crack, 7 to 8 minutes. Let cookies cool completely on sheets, about 2 hours. Serve.