Place water, chiles, onion, vinegar, ketchup, garlic, and salt in a saucepan; bring to a simmer, and cook, stirring occasionally, until reduced and very thick, about 1 hour.
Pour chile mixture into a blender no more than half full. Cover and hold lid down; pulse a few times before leaving on to blend until smooth. Stir cream into chipotle sauce; refrigerate until ready to use.
Place eggs in a saucepan; cover with water. Bring to a boil, remove from heat, and let eggs stand in hot water for 15 minutes. Remove eggs from hot water, cool under cold running water, and peel.
Place bacon in a large skillet; cook over medium-high heat, turning occasionally, until evenly browned, about 10 minutes. Drain bacon on paper towels. Crumble half the bacon; reserve remaining bacon for garnish.
Cut each egg in half lengthwise; place egg yolks into a bowl. Mash egg yolks with a fork; stir in mayonnaise, crumbled bacon, and Cheddar cheese. Stir 1 tablespoon chipotle sauce into yolk mixture, or more to taste.
Place egg whites cut-side up on a serving plate. Spoon yolk mixture into egg white halves. Sprinkle remaining bacon over filling; drizzle with chipotle sauce.