I synched for the first time ever with iTunes. This deleted all of my apps. I re-synched with iTunes, and now my apps are back, but no data files.
I am sorry to hear that iTunes deleted all you data! This is not what a sync with iTunes is supposed to do, so I suggest that you also check the forums on Apple's website or ask Apple directly why that happened.
A restore through iTunes overwrites all documents on the iPhone and I do not know of a way to recover them. - If the documents were contained in any previous backup they could be restored from that. You might take a look at
http://code.google.com/p/mobilesync-inspect/downloads/list or
http://supercrazyawesome.com/
to see if their tools could help.
I'm sorry that I have not better solution for you ...
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