Mix together flour, salt, black pepper, paprika, garlic powder, and onion powder in a bowl. Dredge beef short ribs in the seasoned flour mixture. Reserve 3 tablespoons of leftover seasoned flour.

Heat olive oil in a large pot over medium-high heat. Cook beef ribs in hot oil until browned, 3 to 5 minutes per side. Remove ribs and set aside.

Reduce heat to medium and melt butter in the pot. Cook and stir sweet onions in butter until soft and slightly browned, about 15 minutes; reduce heat if onions begin to burn.

Stir reserved seasoned flour into onions. Cook and stir for 10 minutes. Pour in beef broth and sherry; bring to a boil, stirring constantly, until soup is slightly thickened. Season with salt and black pepper.

Strip leaves from thyme sprigs and add them to the soup. Return short ribs to the pot, reduce heat to low, and simmer until ribs are tender, about 2 1/2 hours. Stir soup every hour or so.

Preheat the oven broiler.

Ladle soup into oven-safe soup crocks. Carefully place a short rib into each crock. Top each soup with 2 slices of French bread and sprinkle about 1/4 cup Gruyère cheese over each crock.