Well think of it like this maybe. When Naruto makes one clone, he does actually work and control that clone. Because he has to use part of his energy to control that clone he is limited to his energy, meaning Naruto is now only capable of using 50% of his chakra, the other 50% is going towards controlling the other clone. He is not losing any chakra, he is limiting the amount he can use to control the others. Now if he creates a clone, and someone immediately defeats it, Naruto doesn't have to limit himself to control that one, so he has close to all his chakra back. Does that make any sense?