Preheat the oven to 350 degrees F.
Heat two tablespoons olive oil in a large skillet over a high flame. Saute the squash and shallot until tender and beginning to brown, about 5 minutes. Add the cherry tomatoes and continue to cook until the tomatoes have softened and begun releasing their juices, about 3 minutes more. Stir in the spinach and cook for another few minutes, until wilted. Set filling aside to cool slightly.
Meanwhile, combine the salsa, yogurt, and ½ cup water or stock in a medium mixing bowl and whisk until combined. (NOTE: if the salsa is chunkier, run the ingredients through a food processor).
Ladle half the sauce into the bottom of a 9 x 13 casserole dish (or into two 8 x 8 dishes). Add half the cheese to the squash mixture and stir to combine. Spoon a few heaping tablespoons of the veggies into the center of one of the tortillas. Roll and place seam-side down in the baking dish. Repeat with the remaining tortillas and filling.
Pour the remaining sauce over the enchiladas and sprinkle with the remaining cheese.
Bake in the oven for 20-30 minutes until the cheese is melted and beginning to brown. Serve warm alongside a simple salad