Two reasons: 1. In the beginning, the bacteria count will likely be out of balance. It takes a few days for the good bacteria to take over. Removing part of the starter also removes a good deal of the waste products that make sourdough bread too sour. You will know by the smell who is winning the war. 2. If you were to keep all the flour and water you used in this process, you would need a much bigger jar. As it is, you only need a pint-size glass jar.