Help syncing for first time please

Hi
I have an iPod touch that has loads of apps installed. I want to sync it for the first time to a new itunes installation. I took the option to transfer purchases from the ipod, and can now see the apps in itunes. However, when I tick the option to sync applications, I get a warning that this will erase all applications AND DATA from the ipod. I obviously do not want to lose all the high score data etc. Will it really delete all apps and data and then copy all apps back to the ipod (thereby losing the data)? Or is this just a generic warning regarding syncing, and it will see that all apps match and to leave them alone?
THanks for any help.

You'll need to back up your ipod manually before syncing it to your new iTunes. Here's how to:
Make sure your still authorized in iTunes. Disable autosync in itunes, connect your ipod, right click on it in the device list and choose backup.
This will save data, pictures and settings to itunes. See what's included in this backup here: http://support.apple.com/kb/HT1766
Set up at least one contact and event on your computer to be able the merge your calendars and contacts after your ipod got wiped during the first sync.
The rest of the data can be restored from the backup you made.
Restoring: http://support.apple.com/kb/HT1414
Music is one way only, from the computer to your device, unless you bought the songs in itunes and transferred your purchases.

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