IPAD restores applications but not data or files associated with applications

1) Today Itunes prompted me to update the OS on the IPAD.
2) It warned me to back up IPAD before I did. I did
3) I updated software.
4) It returned with an error saying it could not install software and I must restore to facotry settings
5) I resotored to factory settings
6) After that I attempted to restore contents of my IPAD from Itunes on my Windows 7 machine.
7) It restored only music but no applications and no other information
8) I spent all day on the phone with Apple Support who managed to get the applications restored by going through one by one and syncing.
9) It took a few hours
10) After I finished I noticed that files/documents associated with various applications like Kindle, Goodreader, Penultimate Notes were missing on the IPAD.
11) I have made a few phone calls to Apple and thy claim the following: "Apple is not responsible for restoring files or data associated with any applications, only the application itself. It is your responsibility to contact the application developer to get your files restored." This sounds patently absurd to me. I spent half an hour explaining the absurdity of this claim to the Apple representatives but they are firm and non-wavering in this opinion. One even claimed that restoring does not restore applications which of course is not correct.
12) I gave them the example of MS Word on MacBook Pro. If I save/back up on another machine and then restore back to the original machine I would expect to be able to see the Word files I had created and saved. That in particular the failure to view them would not be Microsoft's responsibility but Apple's. They disagreed saying it would be between me and Microsoft and the Apple devices had nothign to do with saving or successful restoring.
13) So I have lost all e-books purchased on Kindle, plus all documents saved on Goodreader application, notebooks on Penultimate applications, and my children’s drawings on their drawing applications. Apple Support say I should contact each application vendor to try and recover the missing data. They refuse to tell me how to get it from ITUNES backup stored on my Windows 7 machine as they say it will not be there.
They have asked me to write to
Apple Customer Support,
Holly Hill,
Cork,
Ireland
quoting case number 319718819.

Did you try restoring from a backup of the iPad? If you have a backup with all of your app data and files, that should restore all of that content to the device.
No - restoring does not restore applications. You have to either sync the applications back from iTunes on your computer, or you can download them again, BUT ... All of your data, files and device settings are stored in your backup. Do you have a backup in iTunes .... Edit>Preferences>Devices - that should show you all of your iDevice backups.

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http://support.apple.com/kb/ht4097
iTunes: Specific update-and-restore error messages and advanced troubleshooting
http://support.apple.com/kb/TS3694
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