Preheat oven to 350°F.
Heat a Dutch oven over high heat. Season the meat with salt and pepper, and brown in batches to avoid crowding the pan. Remove and reserve.
Lower heat a bit, melt in butter and add vegetables, herbs salt and pepper, and cook until soft, 10 minutes. Sprinkle in flour, cook 1 minute then deglaze pan with wine. Add stock, soy, Worcestershire, cider and reserved beef, bring to boil, cover and transfer to oven. Roast 75 minutes remove and raise oven temp to 400°F. Scrape the bottom of the pan and add a little stock or water if necessary. Stir in apples and roast 30 minutes more. Remove from oven, stir and remove bay and herbs.
While the beef is cooking, make the dough: Add flour, butter, sugar, salt, pepper or mustard, and nutmeg to a food processor and pulse to combine butter into flour. Add enough ice water to form dough; add cheese and pulse. Press dough together, wrap and chill at least 30 minutes.
To make the pot pie, transfer beef filling to a large, casserole dish. Roll out the chilled dough in a large circle on a lightly floured surface. Brush the edge of the casserole dish with egg wash and lay dough on top of beef. Press and crimp around the edges. Trim off the excess and cut a small 1-inch round hole at the center to vent.
Place casserole in oven and bake to golden, about 20-30 minutes. Let stand 10-15 minutes before serve.