Preheat oven to 375 degrees. Prick sweet potatoes all over with a fork. Place on a large piece of foil on a baking sheet; fold foil around sweet potatoes to form a packet. Bake until tender when pierced with a knife, about 1 hour.
When cool enough to handle, halve sweet potatoes lengthwise. Scoop out all but 1/4-inch flesh from inside skins. Arrange 8 skins in a single layer in a 9-by-13-inch baking dish (discard remaining 2 skins). Place flesh in a food processor, along with 2 tablespoons butter and goat cheese; season with salt and pepper. Process until smooth, 2 minutes. Add chives and pulse to combine; spoon into skins.
In a small bowl, stir together pecans, panko, and 2 tablespoons butter until combined; season with salt and pepper. Sprinkle panko mixture over sweet potatoes. Bake until topping is golden, 10 to 12 minutes.