IPad upgrade to iOS 6 lost apps/data

I have just upgraded my iPad 2 to iOS 6.0.1. I backed it up beforehand, but the upgrade has lost virtually all the applications, and their data as well as the music (which I backed up manually beforehand). Is there any way to recover this?

Upgrading iOS
   1. How to update your iPhone, iPad, or iPod Touch
   2. iPhone Support
   3. iPod Touch Support
   4. iPad Support
     a. Updating Your iOS to Version 6.0.x from iOS 5
          Tap Settings > General > Software Update
     If an update is available there will be an active Update button. If you are current,
     then you will see a gray screen with a message saying your are up to date.
     b. If you are still using iOS 4 — Updating your device to iOS 5 or later.
     c. Resolving update problems
        1. iOS - Unable to update or restore
        2. iOS- Resolving update and restore alert messages

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Hi,
I need to sync two different iPad, first gen iPad & iPad 2, on one iTunes.
The iPad 2 has been used for few months, and the apps/games data are said to be wiped out if I sync the iPad 2 with the same iTunes for the first gen iPad.
The iPad 2 has never been synced to iTunes before, and I'm planning to transfer all of the purchases made with it to the iTunes for the first gen iPad.
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Diesel, thanks for your reply.
The iPad 2 was synced to a different iTunes for the activation process, now I'm syncing it to my iTunes in my laptop.
I've solved the problem myself, sort of, when I updated the iPad 2 with iOS 5. The iTunes backed it up first, after the iOS 5 is installed, the iTunes said it has restored the iPad 2. Although when I looked at the iPad 2, all of the apps were gone. I synced the apps in iTunes with iPad 2, and it turns out all of the game's/apps's data was also restored back. Amazing.
Thumbs up to Apple, especially the iOS team.
But I wonder, what if I didn't update it into iOS 5, instead I sync the apps just like that, will the game's/app's data be restored too..

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Hi everyone and thank you in advance to anyone who can offer some help!
Apple recently told me some issues I was having with my phone were software based and they refused to issue me a replacement phone until I attempted to setup the phone as a new phone in iTunes. I did so and it didn't fix the issues. I am waiting on a replacement, however, in the meantime, I am restoring to the backup file from iTunes. I have restored all of my general data but, all of my app data is missing.
I'm most concerned with an app that keeps track of my time off requests for work (including info on all of my vacation days and sick time, from the last 5 years) as I know I have time to take off before the end of the month. I know, it sounds silly.
Bottom line, is there a way to restore the backed-up app data to my phone? I've never had this problem when I've used the backup to set up a new phone or a replacement in the past.
Many thanks!
Note: I have an iPhone 5 and am using a Windows based computer.

The backups are completely random and although I backed up daily and, as a precaution, 4 times previous to the advised restore, there is only one that is current (the next most recent file is from a year ago).
As mentioned, I've previously had no issue with this. I've received replacement phones and purchased upgrades in the past, and never had any issues with app data syncing.
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http://support.apple.com/kb/HT1430
Welcome to Apple Support Communities!
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Delgadoh

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Hi
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http://support.apple.com/kb/HT1766
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http://www.apple.com/support/itunes/contact/
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IPad upgrade to iOS 6 lost apps/data

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