Well, if you are running iOS 5 and syncing with iCloud, you could go into Settings for the app and turn off iCloud. The next time you open the app it will offer you a choice to keep or delete the local files. Delete them.
Later you can go back to Settings and turn iCloud on. The files will sync back to the iPad. If you have a lot, or they are big, it might take a few minutes.
I recommend saving them elsewhere also, just to be safe. Box.net is easy. It works with the WebDAV option.
If you wanted to keep them out your mail, calendars, and such, you can also delete the iCloud account, then sign on again later. That should work with any other type of account as well, but I'd hesitate to do it with a POP account. Sometimes you get more back than you bargained for when you re-add them.