Recently dealt with this problem with my parents upgrading from an iPad 2 to an iPad 3.
The iPad 2 was synced to one laptop, the iPad 3 was destined for another. We synced the iPad 3 to a backup of the iPad 2 and then went to plug it into the new laptop. (NOTE: the new laptop had all files from the old library synced via home share first.) iTunes asked whether to leave it alone or erase the iPad and sync. After playing around and much googling we went ahead and tried hitting erase and sync. When you do this, if the two iTunes libraries have the same iTunes account, it will actually make a full backup of the iOS device BEFORE it "erases and syncs."
Once it was done, all files were there, even each app's files and settings. (Such as PDFs saved in good reader).
This may not have been the case back in 2008 when http://www.iclarified.com/entry/index.php?enid=2137 was posted. But it seems Apple has caught on, and they just need to reword the message box so they don't scare users into thinking they'll lose everything.