Bring a large pot of salted water to a boil. Meanwhile, season the pork chops on both sides with salt and the paprika. Melt 1 tablespoon butter in a large skillet over medium-high heat. Add the pork chops and cook until browned, adjusting the heat as needed so the butter doesn't get too dark, about 2 minutes per side. Remove the pork to a plate.
Add the apples and shallots to the skillet. Cook, tossing, until lightly browned, about 3 minutes. Move the apples and shallots to one side of the skillet and add the tomato paste to the other side. Cook the tomato paste, stirring, until it darkens slightly, about 1 minute. Add the vinegar, honey and thyme, then stir in 1 cup of the boiling water from the pot. Bring to a simmer and cook until the apples are tender and the sauce thickens, 8 to 10 minutes. Add a little more water, if needed.
Meanwhile, add the pierogi to the pot of boiling water and cook as the label directs. Remove with a slotted spoon and transfer to the skillet; nestle the pork chops in the mixture. Cut the remaining 1 tablespoon butter into small pieces and stir into the sauce. Cook, stirring, until the pierogi are coated in the sauce and the pork is just cooked through, about 2 minutes. Divide among plates. Top with chives.