Lost Synch Data

I had a poor internet connection so I was unable to update itunes on my laptop using APPLE SOFTWARE UPDATE - which fails if there are interuptions in your signal. Instead I downloaded the new itunes from apple.com and installed it - not realizing that it would lose all of my iphone synch data. Now I have my iphone filled with dozens of games that I have progressed partially through and books on Stanza and Kindle. I don't want to lose the progress I have made on my games - but if I synch it tells me it will wipe my iphone. I have saved all of the games and apps I own back to my machine. But I just want to be sure that if I synch it and then load the backup, my app data and progress in my games and all of my books in Stanza will not be lost. Otherwise, I don't know what to do because it would take a LONG time to regenerate everything.
It would be MUCH better if Apple would let us synch to any of our authorized 5 computers without wiping the iphone everytime, but that would make life too easy...
Thank you

Welcome to the discussions,
You'll have to back up manually. All 3rd party data is stored in the backup made by iTunes. More info on the content here: http://support.apple.com/kb/HT1766
To back up manually, disable autosync in iTunes/settings/devices. After that connect your phone, right click on it in the device list and choose "backup". A backup without the sync process will be created.
To be sure that your apps are copied as well, right click again, this time choose "transfer purchases".
After your phone got wiped due to the new setup, use the manual backup to restore from.
To be sure your backup does not get overwritten, copy the backup folder to a save location, you can find it here:
Mac: ~/Library/Application Support/MobileSync/Backup/
Windows XP: \Documents and Settings\(username)\Application Data\Apple Computer\MobileSync\Backup\
Windows Vista and Windows 7: \Users\(username)\AppData\Roaming\Apple Computer\MobileSync\Backup\

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