Step 1In the bowl of a food processor, pulse the whole-wheat and all-purpose flours, 1 teaspoon salt and one-half teaspoon black pepper to combine. Add the butter and pulse until the butter is reduced to pea-sized pieces.
Step 2In a measuring cup, whisk together the vinegar and egg yolk (reserving the egg white) and add enough ice-cold water to bring the volume to one-half cup. Add the liquid to the processor in a steady stream while pulsing.
Step 3Continue to pulse just until the mixture looks crumbly and damp, and the dough just adheres when pressed together. Turn the dough out onto a sheet of plastic wrap and press into a disk. Wrap tightly and refrigerate for at least one hour, up to overnight.
Step 4Heat the oven to 400 degrees.
Step 5Bring a large pot of salted water to a boil and blanch the dandelion greens, in batches, for about 1 minute to bring out the color and soften slightly. Run the greens under cold water and chop coarsely. Squeeze the chopped greens in a towel to remove as much liquid as possible and set aside.
Step 6In a large saute pan, cook the onions and leeks in the olive oil over medium heat until soft, 8 to 10 minutes. Add the garlic and continue to cook until the garlic is aromatic, about 1 minute. Stir in one-fourth teaspoon salt, the pepper flakes, one-fourth teaspoon black pepper and the cayenne. Remove from heat and cool.
Step 7In a large bowl, combine the cheeses, dandelion greens and onion mixture.
Step 8Divide the chilled empanada dough into 8 disk-shaped portions. On a floured work surface, roll out each portion of dough into an approximately 7-inch circle. Place one-third cup of the filling in the lower middle section of the circle. Whisk the reserved egg white in a small bowl and use it to brush the outer edges of the lower half of the dough. Fold the dough in half over the filling, pressing the edges and making sure there are no air pockets. Trim any rough or uneven parts and either crimp the edges with your fingers or use a fork to seal the edges.
Step 9Place the empanadas on a parchment-lined baking sheet. Brush the empanadas with the egg wash and sprinkle with coarse sea salt. Bake until puffed and golden, 25 to 30 minutes. Cool on a rack. The empanadas will keep, refrigerated, for up to 2 days.