Preheat the oven to 425 degrees F. Line a baking sheet with parchment paper.
Whisk the eggs together with the milk. Add a drizzle of oil or a pat of butter to a skillet over medium heat. Add the eggs and scramble until just set. Season with salt and pepper. Remove from heat and let cool while you make the dough. It is important to let the eggs cool before filling the dough.
In a large bowl, whisk together the flour, salt, and baking powder.
Add the cottage cheese to a blender or food processor and blend until smooth. Pour the blended cottage cheese into the flour mixture and stir to combine. Use your hands to fully bring the dough together. The dough will feel a little dry and flakey at first, that is normal. If the dough feels too dry, add 1-2 tablespoons more of blended cottage cheese. Form it into a ball.
Flour a large, clean surface. Add the dough and roll it out to roughly 24 inches long in a rectangle shape. Make one cut lengthwise down the center, then two horizontal cuts to create 6 equal pieces.
In the center of each piece, add a portion of scrambled eggs, one slice of cooked bacon, and shredded cheese. Carefully pull all the sides of the dough up and around the filling, pinching them together to create a sealed ball shape. Place seam side down on the prepared baking sheet.
Whisk one egg together in a small bowl. Brush each pocket with egg wash and sprinkle generously with everything bagel seasoning.
Bake for 15-20 minutes or until the tops are golden brown. Let cool slightly before serving.