Safari tends to hold references to cache cookies/history and databases in RAM, you can check this by restarting Safari. Cookie does in fact physically remove all these items from disk, but i don't know of a way to 'force' Safari to update its internal references.
Thank you for the response. If Cookie removes this information from disk, but Safari keeps the information in Ram, does this mean that tracking still occurs at some level? Or is the physical removal of this information from disk by Cookie enough?