In a large bowl, combine the flour and salt. Make a well in the center and add the egg, sour cream, and water. Mix until a dough forms. Knead the dough on a floured surface for about 5 minutes until smooth. Cover with a kitchen towel and let it rest for 30 minutes.
While the dough is resting, cook the bacon in a large skillet over medium heat until crispy. Remove the bacon and drain on paper towels, leaving the drippings in the skillet.
In the same skillet, add the sliced onions and butter. Cook over medium-low heat, stirring occasionally, until the onions are caramelized and golden brown, about 15-20 minutes. Season with salt and pepper to taste. Remove from heat and stir in the cooked bacon.
Roll out the rested dough on a floured surface to about 1/8 inch thick. Use a round cutter or a glass to cut out circles (about 3 inches in diameter).
Place a small spoonful of the cheddar cheese and onion-bacon mixture in the center of each circle. Fold the dough over to create a half-moon shape and pinch the edges to seal tightly.
Bring a large pot of salted water to a boil. Drop the pierogies in batches into the boiling water. Cook for about 3-4 minutes or until they float to the top. Remove with a slotted spoon and set aside.
In the same skillet used for the onions, add the cooked pierogies and sauté for 2-3 minutes until they are golden brown on both sides.
Serve warm, garnished with chopped chives if desired.