Melt the butter in a large Dutch oven or pot over medium heat. Add the onion and cook until tender, about 5 minutes. Whisk in the flour and cook until golden, 3 to 4 minutes, then gradually whisk in the half-and-half until smooth. Add the chicken broth, bay leaves and nutmeg, then season with salt and pepper and bring to a simmer. Reduce the heat to medium-low and cook, uncovered, until thickened, about 20 minutes.
Meanwhile, prepare the bread bowls- Using a sharp knife, cut a circle into the top of each loaf, leaving a 1-inch border all around. Remove the bread top, then hollow out the middle with a fork or your fingers, leaving a thick bread shell.
Add the broccoli and carrot to the broth mixture and simmer until tender, about 20 minutes. Discard the bay leaves. Puree the soup in batches in a blender until smooth; you'll still have flecks of carrot and broccoli. Return to the pot. (Or puree the soup in the pot with an immersion blender.)
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