COOK ONIONS Arrange beef bones on paper towel-lined plate. Microwave until well browned, 8 to 10 minutes. Meanwhile, set slow cooker to high. Add butter, cover, and cook until melted. Add onions, 2 teaspoons salt, 1 teaspoon pepper, brown sugar, and thyme. Stir flour, apple butter, sherry, and soy sauce together in small bowl until smooth. Pour over onions and toss to coat. Tuck bones under onions around edge of slow cooker. Cover and cook on high heat until onions are softened and deep golden brown, 10 to 12 hours. (Cooked onions can be refrigerated in airtight container for 1 day.).
2. FINISH SOUP Remove bones from slow cooker. Heat chicken and beef broth in microwave until beginning to boil. Stir into slow cooker. Season with salt and pepper.
3. MAKE CROUTONS Adjust oven rack to upper-middle position (about 6 inches from broiler element) and heat oven to 400 degrees. Arrange bread slices in single layer on baking sheet and bake until bread is golden at edges, about 10 minutes. Heat broiler. Divide cheese evenly among croutons and broil until melted and bubbly, 3 to 5 minutes.
4. SERVE SOUP Ladle soup into bowls and top each with 2 croutons. Serve.
**Most soup recipes start by chopping or mincing onions. For this recipe, we wanted slices that would retain their shape through 10 to 12 hours of gentle simmering. We found that cutting onions with the grain (rather than across it) yielded slices durable enough for the slow cooker.