In a large skillet on the stove-top set on medium heat add the diced bacon and slowly cook the bacon until crispy. Remove the cooked bacon with a slotted spoon and set aside on a plate lined with paper towels to drain.
Pour off the bacon fat from the skillet except for about 2 tablespoons and add the chopped onion. Cooked the onion over medium-high heat until the onion becomes translucent and starts to just turn brown.
Add half of the bacon, onions, chicken stock, potatoes, celery, carrots, garlic, bay leaves, thyme and pepper to a 6 quart or larger slow cooker and stir to combine.
Cover and cook on LOW for 6 to 8 hours or on HIGH for 3 to 4 hours or until the potatoes and carrots are soft.
During the last half hour of cooking whisk together the sour cream, half and half and flour until there are no lumps of flour.
Remove and discard the bay leaves.
Add the cream mixture and shredded cheddar cheese to the soup and stir to combine.
Recover and continue cooking on LOW for the remaining 30 minutes until the soup is thickened.
Ladle hot soup into bowls and garnish with chopped chives and a sprinkle of the reserved bacon.