One of your most important tasks is to track the flow of documents through the data preparation process. A large job, such as a 20 to 30-volume encyclopedia, might consist of 20 MB of data broken into thousands of individual files. You may have to pass each file through a dozen or more conversion stages.
There is no need to save every stage forever—you could have 100,000 files—but you shouldn't start deleting until certain the last stage is error free. If an error does pop up, you'll want to be able to retrace the path and spot the cause.