Concerned about losing App Data after moving to new PC

I've reinstalled iTunes to a new Windows 7 machine, and de-authorised the old installation on the old XP machine.
In the App tab there are no apps at all listed in the left pane, and on the right pane there are images of my iPhone with the apps all in place.
If I click the Sync Apps box it says "are you sure, all existing apps and their data from this phone will be removed will be replaced with apps from this iTunes library.
This concerns me because looking at the apps pane or opening the Apps window in the Library, shows an empty screen.
I have a backup from the old installation, and I looked in the Windows 7 location, and their is a backup in there with exactly the same name and almost the same size.
I'm tempted to tick the sync apps button, but am concerned I'll lose all the app data, that would be a bit of an issue.
Any advice?

Ok I think I have a problem here :o(
When I do the transfer from phone, at the top of itunes it says "Copying 1 of 22:Happy" then it freezes and eventually times out saying
+Attempting to copy to disk "Itunes" Failed : Device timed out"the drive did not respond.+
Two things wrong with that, obviously the hang, and also there are a lot more apps than 22.

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Reset iPod touch: Hold down the On/Off button and the Home button at the same time for at
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Apple will exchange your iPod for a refurbished one for this price. They do not fix yours.
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I forgot to mention that I am running iTunes on a Windows 7 PC.
I put this in a reply because I couldn't find out how to edit the post.

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Concerned about losing App Data after moving to new PC

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