Add the cottage cheese, vanilla, and cocoa powder to a food processor/blender and puree until completely smooth and blended. This blooms the cocoa into the moisture and deepens the chocolate flavor. Set aside.
In a stand mixer, beat the softened butter, peanut butter, and both sugars together for about one minute, until combined. Scrape down the bowl.
Add the egg yolks and mix for another minute. Scrape down the bowl.
Add the sourdough discard and mix until incorporated.
Add the pureed cottage cheese mixture and mix until incorporated.
In a separate bowl, whisk together the bread flour, instant coffee, baking soda, cornstarch, and salt.
Add the dry ingredients to the wet and gently mix just until the dough comes together and looks shaggy. Do not overmix.
Add the chocolate chunks/chips and mix until just incorporated, holding back a small handful for the tops.
Chill the dough at least 2 hours, up to overnight or about 12 hours for the best flavor.
Scoop the dough into thick mounds, about 70 grams each. Form a firm ball, press a few chocolate chunks onto the top, then dip just the top into granulated sugar. Place sugar side up on a lined baking sheet and gently press down into a thick disc.
Bake at 350 degrees Fahrenheit for 10 to 12 minutes, until the edges are set but the centers still look slightly underdone. You don't want to over bake these.
Let the cookies set on the pan for a few minutes before moving them. They firm up as they cool.