One application is often reason enough to stop people from switching from Windows to Linux or Mac.
Similarly, something as severe as the chance of corrupting their iPod can easily make people wait a few days to upgrade to Vista. It is just Apple's advice. You are free to ignore it and risk losing your iPod.
You don't know how crazy some people can be about iTunes, iPod and their song collection. Telling such a person to avoid using iTunes for a week is disaster for him. Ultimately, the decision rests with you. You have to decide which is more important - Windows Vista or your iPod.
