Microwave Potatoes: Place the baby potatoes in a microwave-safe bowl with the water. Cover the bowl tightly with plastic wrap and microwave until the potatoes are fork-tender, about 5 to 7 minutes.
Chop Chives: Finely chop the chives on a cutting board. Set aside a small pinch for garnish and save the rest for the filling.
Cube Cheese: Cut the cheddar cheese into 12 small cubes, making sure each cube is small enough to fit inside a baby potato.
Hollow Potatoes: Cut a small slice off the top of each cooked potato. Use a small spoon to scoop out the center of each potato, making a little potato cup.
Arrange Potatoes: Place the hollowed potatoes upright on a tray so they are ready to fill.
Add Cheese: Place one small cube of cheddar cheese into the center of each potato while the potatoes are still warm.
Season Potatoes: Sprinkle the potatoes with kosher salt, then drizzle them with olive oil.
Mix Filling: In a small mixing bowl, combine the sour cream, softened cream cheese, black pepper, bacon bits, and most of the chopped chives. Stir with a spatula until the mixture is creamy and evenly combined.
Top Potatoes: Spoon the cream cheese mixture onto each filled potato bite.
Garnish and Serve: Sprinkle the reserved chopped chives over the potato bites. Serve warm so the cheddar softens inside each potato.