Preheat oven to 450°F.
Cut the neck of the butternut squash from the base; reserve the base for roasting or soup. Using a mandoline or sharp knife, cut the neck of the butternut squash into slices an 1/8-inch. Arrange them onto 2 to 3 parchment-lined baking sheets, making sure they don’t overlap. Drizzle with oil or spray with cooking spray and season with salt, and pepper. Bake for 10-12 minutes, flip and bake another 6-8 minutes until brown and crispy on edges.
For the onions, preheat olive oil in a large skillet over medium-high heat. Add onions, thyme, salt and pepper, and stir to combine. Lower the heat to medium and cook until onions begin to turn caramel in color, about 20-25 minutes.
Add cranberries, jalapeño, onion, cilantro, lime zest and juice, honey, salt and pepper to a food processor bowl and pulse to desired consistency. (Salsa can be made 1-2 days ahead and stored in an airtight container.)
Arrange butternut chips on a clean baking sheet then top with caramelized onions and blue cheese crumbles. Place under the broiler until blue cheese has melted. Top with cranberry salsa and pecans, and serve from baking sheet.
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