Roast the Squash: Preheat your oven to 400°F (200°C). Toss the diced butternut squash with a drizzle of olive oil, salt, and pepper on a baking sheet. Roast for 15-20 minutes until tender and caramelized edges appear. Remove and set aside. Note: This step develops sweetness that boiling cannot achieve.
Cook the Protein: While the squash roasts, heat a large oven-safe skillet over medium-high heat with a little oil. Add the chicken cubes in a single layer. Season with salt and pepper. Cook for 3-4 minutes per side until golden brown and cooked through (internal temperature of 165°F/74°C). Remove chicken from the pan and set aside on a plate.
Sauté Aromatics: Reduce heat to medium. In the same skillet, add the diced onion and carrots. Cook for 5-7 minutes until softened. Add the garlic and cook for 1 minute more until fragrant.
Make the Roux: Sprinkle the flour over the vegetables and stir constantly for 1-2 minutes to cook off the raw flour taste. Gradually whisk in the chicken broth, scraping up any browned bits from the bottom of the pan. Continue whisking until the mixture begins to thicken slightly.
Create the Sauce: Reduce heat to low. Stir in the heavy cream, thyme, and sage. Simmer gently for 2-3 minutes until the sauce coats the back of a spoon. Taste and adjust seasoning with salt and pepper as needed.
Combine Filling: Return the cooked chicken and roasted butternut squash to the skillet. Stir gently to combine everything in the creamy sauce. Remove the skillet from heat. Let the filling rest for 10 minutes; this thickens the sauce further and makes it easier to handle without being runny.
Prepare Pastry: Preheat oven to 425°F (220°C). On a lightly floured surface, roll out the thawed puff pastry sheet just enough to fit your skillet diameter if necessary. Carefully drape the pastry over the hot filling in the skillet, tucking the edges down slightly. Trim any excess hanging over the edge.
Bake: Brush the top of the pastry generously with the egg wash. Use a knife to cut three small slits in the center for steam vents. Bake for 20-25 minutes until the pastry is puffed, golden brown, and crisp.
Rest and Serve: Let the pot pie cool in the skillet for 5-10 minutes before slicing. This allows the filling to set so it doesn't spill out when cut. Sprinkle with flaky sea salt if desired, then serve warm.