Heat a pot of water to boil for the pasta. Salt the water,then add the pasta and cook al dente, about 8 minutes.
While the pasta cooks, heat a medium heavy-bottomed pot over medium heat. Add the olive oil and butter. When the butter melts into the oil, add the thyme and grate the onion directly into the pot with a Microplane or grater. Cook the onions for a minute or two.
Add the flour and cook with the onions a minute or two more.
Whisk in the stock, then add the squash and cook until warmed through and smooth.
Stir in the cream and bring to a bubble.
Stir in the cheeses in a figure eight motion and season with salt, pepper and nutmeg. Taste to adjust seasonings.
Drain the cooked pasta well and combine with the sauce. Serve.