Preheat the oven to 355°F/180°C. Line a baking sheet with parchment paper.
In the bowl of a stand mixer fitted with the paddle attachment, combine the flour, butter, Parmesan, Emmental, and sesame seeds. Mix on medium-low speed just until a cohesive dough forms—do not overmix.
Transfer the dough to a clean surface and divide it into three equal portions. Roll each portion into a compact log about 1½ inches (4 cm) in diameter. Wrap each log tightly in plastic wrap and freeze for 30 minutes, until firm.
In a wide shallow bowl, combine the nigella seeds, sesame seeds, and Parmesan flakes.
Unwrap the dough logs. Using a pastry brush, coat each log evenly with beaten egg. Roll each log in the seed mixture, pressing gently so the coating adheres well.
Using a sharp knife, slice each coated log into ¼-inch (6 mm) rounds. Arrange the slices on the prepared baking sheet, spacing them about ½ inch (1 cm) apart. The cookies will not spread much.
Bake for 15 minutes, or until golden and crisp around the edges. Let cool on the baking sheet for 5 minutes, then transfer to a wire rack to cool completely.
Store in an airtight container at room temperature for up to 5 days.