Scrub the beets and put them on a large sheet of aluminum foil; season with salt & pepper, and drizzle with 2 tablespoons of olive oil. Enclose the beets in foil, place them on a baking pan (to prevent dripping), and bake until the beets are tender, about 1 hour. Set aside. When the beets are cool enough to handle but are still warm, peel off their skins and cut them into 1/4-inch dice.
In a large heavy bottomed pot set over medium heat, add the bacon and cook until it begins to brown, about 3 minutes. Add the remaining tablespoon of olive oil, the onion, carrots, and parsnips, and cook until the vegetables are softened and just starting to color, about 10 minutes. Add the thyme, stock, cabbage, and beets and simmer until the vegetables are tender, about 20 minutes. Remove the thyme sprgs. Add the vinegar, honey, and apple. Season with salt & pepper.
To serve, mix the dill and sour cream. Serve the borscht, hot or cold in bowls, garnished with a dollop of dilled sour cream, and sprinkle with a little fresh dill.
The soup can be made ahead up to 2 days and kept covered in the refrigerator. Reheat over medium heat if serving warm. Garnish with the dilled sour cream right before serving.