Add the diced potatoes, diced onion, minced garlic, chicken broth, salt, black pepper, dried thyme, and smoked paprika to the slow cooker. Stir to combine.
Cover and cook on low for 5 to 6 hours, or until the potatoes are very tender.
In a small bowl, whisk together the whole milk and all-purpose flour until smooth.
Once the potatoes are tender, use a potato masher to mash some of the potatoes in the slow cooker to your desired consistency, leaving some chunks for texture.
Stir the milk and flour mixture into the soup in the slow cooker.
Add the unsalted butter, shredded cheddar cheese, shredded mozzarella cheese, and sour cream to the slow cooker. Stir until the cheese is melted and the soup is creamy.
Cook uncovered on low for an additional 15 to 20 minutes, stirring occasionally, until the soup thickens slightly.
Taste and adjust seasoning with additional salt and pepper if needed.
Serve the soup hot, topped with crumbled bacon.