In a large pot or Dutch oven over medium heat, cook the diced bacon for 8-10 minutes, or until crispy. Using a slotted spoon, transfer the cooked bacon to a paper towel-lined plate. Reserve about 1 tablespoon of bacon grease in the pot, discarding the rest.
Add the jalapenos and onions. Cook for 3-5 minutes, or until softened. Add garlic. Cook for 1 minute.
Stir in flour and continue cooking, stirring constantly for 1 minute. Slowly drizzle in chicken broth and milk. Stir until no flour lumps remain.
Add potatoes. Cover and reduce heat to medium-low. Simmer for 20-22 minutes, or until potatoes are fork-tender.
Add creamed corn, sweet corn, salt, pepper, and crushed red pepper flakes. Stir to combine.
Carefully transfer ½ of the soup and cream cheese to a blender and blend until smooth. (Be careful, the liquid will be hot.) Or, use an immersion blender.
Return the blended soup to the pot. Add the cheddar cheese and half of the cooked bacon. Stir to combine and cook for 3-5 more minutes or until the cheese is melted.
Serve hot, garnished with chives and the remaining bacon.