How to keep application data when synchronizing iPhone with new iTunes?
The last time I did this, I still had all my apps but the in-app purchases got lost as well as any saved progress in my games.


To avoid this occasion, you have to save the app data manually. You can do it with any iOS file manager on PC (with i-FunBox for example).

There's one more way to backup the application data: the DataDeposit app from Cydia store uploads all the data of an application to Dropbox and is able to restore it automatically (jailbreak is required).