It should not, but you should always backup the iPad and save any important files anyway; because stuff happens.
Depending on how old your iOS version is, it may require a return to factory (under the new iOS) and then restore from a backup. While this process was (mostly) hidden from the user, the iOS 4 to iOS 5 upgrade did this. So, if you are coming from iOS 4, the backup and saving of files off the iPad is not just recommended, but essential.
Hold in mind that no mater what happens you will be able to recover your apps and most content purchased through the iTunes Store. However, files in those apps are at greater risk. Don't just depend on the backup. Save them individually to a computer or cloud site first.
{I'm pretty sure it was the iOS 4 to iOS 5 upgrade that required several steps in iTunes, including a backup, install of the OS, restore from backup, and then sync. If you accidently stopped the process at the wrong point you ended up with a clean install of iOS 5.}