Turn bacon on saute mode. Meanwhile, cut bacon into small pieces. Once hot, add bacon to the instant pot. Cook until crisp. Remove bacon from instant pot to a paper towel lined plate. Leave bacon grease in instant pot. Add onion, garlic, salt, pepper and dried thyme. Cook, stirring often, for 2 to 3 minutes until softened.
Add potatoes, baby clams and their juices, clam juice, chicken broth to the instant pot. Turn off saute mode. Place lid on instant pot and seal the valve. Cook on high manual for 4 minutes. Allow pressure to release naturally for 5 minutes. Then release pressure manually. Once all pressure is released, remove the lid and change back to saute mode.
Whisk together the half and half and flour. Once the soup is simmering add to the instant pot. Simmer until slightly thickened. Ladle into bowls and top with chives and crumbled bacon.