Meanwhile, in a large saucepan combine the squash and 2 1/2 cups of the milk over medium-high heat. Bring to boiling; reduce heat to medium, and simmer until the squash is tender when pierced with a fork, 18 to 20 minutes. Stir together remaining 1/4 cup milk and flour; stir into squash mixture. Bring to boiling; cook until thickened, 2 to 3 minutes. Stir in 1 1/2 cups of the Gruyere until melted; keep warm.