Press Sear/Sauté and adjust the temperature to 425°F (218°C) and the timer to 1 Hour, and let heat for 5 Minutes.
Add the olive oil, followed by half the mushrooms and ¼ tsp each of the salt and black pepper. Cook, stirring occasionally, until golden brown, Cook, stirring occasionally, until golden brown, 6 to 8 Minutes. Transfer the mushrooms to a plate. Repeat this step with the remaining mushrooms and remaining ¼ tsp each salt and black pepper, adding more oil, if needed. Set the mushrooms aside.
Reduce the temperature to 350°F (175°C). Add the butter and onions to the cooking pot, cover with the lid, and cook, stirring occasionally, until very tender, 12 to 15 Minutes. Uncover, increase the heat to 400°F (205°C), and continue cooking until the onions turn golden brown, 10 to 15 Minutes more.
Sprinkle the flour over the onions in the cooking pot and cook and stir for 1 Minute. Add the wine, increase the heat to 425°F (220°C), and simmer until the liquid has reduced by half, about 8 Minutes. Press Cancel.
Add the beef to the cooking pot along with the broth and all but 2 thyme sprigs. Cover with the lid, press Slow Cook, choose the High setting, and adjust the timer to 5 Hours. Cook until the beef is tender, 4½ to 5 Hours. Press Cancel.
Remove and discard the thyme sprigs from the cooking pot. Stir in the mushrooms and let sit until heated through, about 3 Minutes.
Make your croutons 10 Minutes before serving. Heat the broiler of your oven and linea broiler-proof baking sheet with nonstick aluminum foil. Remove the leaves from theremaining 2 thyme sprigs.
Arrange the baguette slices on the prepared baking sheet and broil until crisp, butnot brown, 1 Minute per side. Sprinkle the slices with the Gruyère and thyme leaves,and broil until the cheese is melted and beginning to brown, about 1½ Minutes.
Ladle the stew into bowls and top with the croutons.