Prepare Potatoes: Wash and dice the red potatoes into bite-sized pieces. Place them in the slow cooker.
Cook Bacon and Onion: In a skillet over medium heat, cook the chopped bacon until crispy. Using a slotted spoon, take out the bacon and set it aside, while retaining the bacon fat in the skillet. Add the diced onion to the skillet and sauté until it becomes tender, approximately 5 minutes.
Make the Dressing: Sprinkle the flour over the cooked onions in the skillet, stirring to coat evenly. Cook for 1 minute, then add the sugar, brown sugar, salt, and pepper. Stir to combine, then add the cider vinegar and water, whisking continuously until the mixture is smooth. Bring to a simmer and cook for 2-3 minutes, or until slightly thickened.
Combine in Slow Cooker: Pour the dressing over the potatoes in the slow cooker. Add the cooked bacon and stir to mix everything evenly.
Cook in Slow Cooker: Cover and cook on low for 4-5 hours, or until the potatoes are tender.
Garnish and Serve: Stir the potato salad gently, adjusting seasoning if needed. Garnish with minced fresh chives if desired, and serve warm.