Preheat oven to 325°F.
Place the bacon in a dutch oven or large pot over medium heat. Cook until crisp. Remove and place on a paper towel lined plate.
Meanwhile, cut the short ribs into ¾ inch pieces. Season with salt and pepper. After the bacon is done, cook the short ribs in the bacon fat until browned on all sides. Cook in batches if necessary (I cooked them in 3 batches). Remove the beef after it has finished cooking and place on a plate.
After the beef has finished cooking, add the mushrooms to the pot. Cook until soft, about 6–8 minutes. Remove and place on a plate.
Place the butter in the pot and allow to melt. Whisk in the flour and cook, stirring occasionally, for 2 minutes. Whisk in the red wine and beef stock. Bring to a simmer.
Add the Dijon mustard, lemon juice, and thyme, along with ½ teaspoon kosher salt. Whisk to combine.
Add the pearl onions, bacon, beef, and mushrooms, and stir to combine.
Cover the pot and place in the oven for 2 hours, or until the beef is tender.
Remove the pot and transfer the mixture to a 1.75 quart baking dish (mine was 10.5x7 inches). An 8x8 inch baking dish works well here, too.
Increase the oven temperature to 400°F.
Roll the puff pastry out and cut to fit the dish with a ½ inch overhang, trimming if necessary. Score the puff pastry in a diagonal pattern with a knife. Brush with the beaten egg. Gently place the puff pastry over the dish and press lightly on the edges to seal.
Bake for 20–25 minutes, or until the top is golden brown. Garnish with fresh parsley and serve immediately.