In a large saucepan, cook the bacon over medium heat until crispy, about 8 to 10 minutes. Use a slotted spoon to transfer the bacon to a paper towel-lined plate and refrigerate until the soup is ready. Pour off all but 2 tablespoons of the bacon fat from the pot.

Add the onions to the remaining fat in the pot and cook until softened and lightly browned, 7 to 9 minutes. Stir in the garlic and thyme, and cook until fragrant, about 30 seconds. Add the broth, scraping up any browned bits, and bring the mixture to a boil over high heat.

Place the potatoes and 1½ teaspoons of salt in the slow cooker. Pour the hot broth mixture over the potatoes and stir to combine. Cover and cook until the potatoes are tender, 5 to 6 hours on high, or 6 to 7 hours on low.

Use an immersion blender to puree the soup until smooth, about 1 minute. (Alternatively, puree the soup in batches using a standard blender, then transfer it back to a Dutch oven and keep warm over low heat.) Whisk in the cheddar until melted, followed by the cream, chives, and 1 teaspoon of pepper. Season with salt to taste.

Microwave the bacon until hot and crispy, about 30 seconds. Serve the soup garnished with the bacon and sour cream.