Microwave the sausage, onion, garlic, thyme, and pepper flakes in a bowl, stirring occasionally, until the onion starts to soften, about 5 minutes. Place the onion mixture in your slow cooker. Add the broth, water, mushrooms, dried beans, bay leaves, and 1/4 teaspoon of salt. Stir to combine. Cover and cook until the beans are tender, 9 to 11 hours on low or 6 to 8 hours on high.