Hi Claire, while technically it will work either way, we think the risk of refrigerating the small dough balls is that they will dry out more quickly, which will limit your optimum refrigeration time to something more like 24 hours. Some bakers also think refrigerating the dough balls will give you less flavor development, but we haven't tested that theory. Perhaps a good compromise would be to refrigerate the cookie dough in 2 smaller containers, which will reduce the time it takes for the dough to soften after refrigeration, while preventing the dough from drying out too quickly in the fridge. 

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