Great question — answering as the UphillTech team:
Your sauce is thickening up too much because it's losing moisture. After you cook your cheese sauce to perfection and mix it in with your pasta 2 things are happening: The sauce loses moisture due to evaporation. It's hot, and even with the lid on you will still lose moisture The pasta will soak up water from the sauce. It's just starch, and starch sponges water up. After being mixed together the pasta will continue to soften by pulling water from the sauce The solution is easy - add more water to replace the lost moisture while it is still warm. When I make this sort of thing I let it cool somewhat and then add pasta water in small amounts until I get a slacker sauce, then I refrigerate or...
Full answer by GdD: https://cooking.stackexchange.com/a/69184 (CC BY-SA 3.0).
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