In a medium bowl, stir the flour, salt, and black pepper together. Add the beef, and then stir to coat. Set aside.
Heat the oil in a Dutch oven over medium heat, and then add the bacon. Allow the bacon to cook in the hot oil until crispy. Dump the seasoned beef into the bacon, and cook until browned, about 6 minutes.
Pour in the red wine, bone broth, and tomato paste. Take care to scrape any browned bits off the bottom of the pan. Add the bay leaves and thyme, and then transfer to the oven. Cook, uncovered, for about 90 minutes.
After 90 minutes, give the stew a stir, and then add the carrots, potatoes, and pearl onions. Continue cooking for a further 30 to 45 minutes or until the vegetables turn tender.
In a small bowl, mix the gelatin with water and allow it to bloom for 5 minutes.
Remove the stew from the oven, and set it back on the stove. Bring it to a simmer over medium heat, and then stir in the bloomed gelatin. Increase the heat to medium-high, and simmer until slightly thickened - about 3 minutes.
Pluck out the bay leaves, and then serve hot. Store any leftovers in a tightly sealed container in the fridge for up to 5 days.