Meanwhile, finely chop the reserved squash flesh. Heat a 10-inch cast-iron skillet over medium heat and add the remaining tablespoon of olive oil. When the oil shimmers, add the chopped squash, shallot, garlic, remaining 1/2 teaspoon salt, and 1/4 teaspoon of pepper. Cook, stirring occasionally, until tender and browned, 2 to 3 minutes. Add the corn, limas, pecans, and thyme. Cook until heated through, approximately 1 minute. Divide the stuffing evenly among the cooked squash and serve immediately.