Device timeout while syncing ipad to itunes

With a USB connection from my iPad3 to my desktop (running the latest version of iTunes), I started a syncing process that went successfully thru 6 of 7 steps. The 7th step seemed to be taking a long while (maybe 20 minutes) and finally timed out with the follow message on a pop-up window on the desktop "Attempted to copy the disk 'OS failed''. The device timed out.". After closing the message window the iTunes desktop app went into a mode of 'Canceling Sync'. It's been in that mode for over 30 minutes now.
My questions:
1. What would cause the time out message in step 7 of 7? (The physical device connection was not the problem)
2. Will I do any damage/corruption to my iPad if I kill the iTunes program while it is in the "Canceling Sync" mode. I may be wrong but it looks like it will never end.
Thanks for any help! Bill OC

App date is stored in the backup that iTunes makes at the beginning of each sync. The apps themselves are stored in the library and not update with each sync. See the following:
http://support.apple.com/kb/HT4079

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