Preheat oven to 400 degrees. Melt the butter in a 10-inch skillet over medium heat. Add onion and cook, stirring, just until tender, about 5 minutes. Add the flour, and cook, stirring for 1 minute. Whisk in the chicken broth or stock and bring to a simmer.
Reduce the heat to low and cook until thick and bubbly, stirring constantly, 2 to 3 minutes. Stir in the butternut squash, thyme, sage, salt and pepper and simmer for 10 minutes, or until the squash is just tender. Stir in the cream and the chicken and return to a simmer. Remove from heat.
While the filling is simmering, make the topping: In a medium bowl, combine the flour, baking powder and salt. Add the butter and cut butter into flour in the mixing bowl using a fork or a pastry cutter until it resembles rough crumbs. Stir in the sage. Add the milk and stir just enough to combine.
Drop dough in 12 mounds on top of the filling in the skillet. Bake for 20 minutes, or until bubbly and the topping is cooked through.