According to a report from The Wall Street Journal, this was revealed during the class-action antitrust lawsuit that was brought against Apple. According to the report, it seems that back in 2007-2009 whenever an iPod was synced with iTunes, it would check to see if there was music obtained from other sources.
If there was, iTunes would keep displaying an error until users were forced to reset their iPods to the factory settings, ultimately erasing all content in the process. Apple has since admitted that this is the case, but they claim that the deletions were intended as a security measure to protect both the user and the device.
However users claimed that this was a monopolistic behavior by Apple and violated antitrust laws. The class-action lawsuit brought against Apple is said to be worth $350 million should Apple be found guilty which is admittedly a rather hefty sum, despite the huge treasure chest that Apple is currently sitting on.