How to keep application data when synchronizing iPhone with new iTunes?

Question

I want to enable app-synchronization between the iPhone and iTunes on a new computer.
I already transferred the apps from the iPhone to iTunes but when checking the box for synchronizing apps, iTunes still displays the warning message that the phone apps will be replaced by the iTunes apps.
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.
This meant that I had to re-download the maps of my navigation app (skobbler). I'd like to avoid this as my monthly data volume is currently very limited.

Is there a way to synchronize without losing the application data?

Answer 1

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).

Answer 2

This problem is solved with iTunes version 11.
It simply offers a checkbox to synchronize new apps automatically and that just works as expected.
I did this on 2 different Windows machines (Win7 and Win8) with the same iPhone and no application data got lost. It seems to me like this means that an iPhone no longer has to be app-synchronized with one iTunes installation.