Preheat the oven to 375°. Cut a thin slice off the tops of the zucchini and reserve. Using a small spoon, scoop out the flesh and finely chop it. Season the zucchini cups with salt and pepper and turn upside down to drain for 15 minutes. Set the cups right side up on a baking sheet and bake for 20 minutes.
Heat the olive oil in a large skillet. Add the bacon and cook over low heat until the fat is rendered, about 4 minutes. Add the onion, red pepper and garlic, cover and cook until softened, about 8 minutes. Add the ground pork, season with salt and pepper and cook over moderately low heat, breaking up the meat, until it is mostly white. Add the eggplant and cook, stirring occasionally, for 5 minutes. Add the chopped zucchini and cook for 10 minutes longer. Remove from the heat and stir in the bread crumbs, olives, basil, Parmesan, sun-dried tomatoes and thyme.
Mound the stuffing in the zucchini cups, top with the lids and bake in the oven for 50 minutes. Serve hot, warm or at room temperature.
If using long zucchini, halve them lengthwise and don't prebake. Stuff and bake in the oven for 15 minutes.
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