Remove stems from mushrooms, reserving mushroom caps for the Mushroom Beef Bites. Finely chop the stems and set aside.
Trim fat from meat. Season all over with salt and pepper. Heat oil over medium-high heat in Dutch oven or large heavy pot; add beef and brown all over. Remove beef and set aside. Drain all but 2 tbsp fat from pan.
Add bacon, chopped mushroom stems and cook, stirring until translucent, about 10 minutes. Add onions, garlic, thyme, salt and pepper. Cook until onions are softened, about 2 minutes. Pour in red wine and beef broth. Return short ribs to pot; bring to boil. Cover and cook in a 325˚F (160 ˚C) oven, until meat is fork-tender, about 1 ½ to 2 hours.
Add ¼ cup parsley; stir to combine. Set aside 2 cups of Bourguignon to make the Mushroom Beef Bites. Use 2 forks to shred the beef bourguignon intended for the Bites; cover and refrigerated for up to three days.

To Make Mushroom Bites

Place mushroom caps hollow side down on parchment paper-lined or greased rimmed baking sheet. Brush caps with some vegetable oil and sprinkle with ½ tsp EACH salt and pepper. Bake in 400˚F (200˚C) oven until slightly softened, about 8 minutes. Let cool slightly and drain off liquid.
Turn mushroom caps hollow side up. Spoon scant tablespoon shredded beef bourguignon into each mushroom cap and heat in 400˚F (200˚C) oven until bubbling. Top with a sprinkling of grated Parmesan and 2 tbsp chopped fresh parsley.