Q: I recently formatted my Windows 7 PC and reinstalled iTunes. I forgot to de-authorize iTunes from my previous Windows installation, so I had to re-authorize my PC as well. When I re-authorized with the iTunes Store and connected my iPad, the “Sync Apps” in iTunes was unchecked. When I click on it to select it I get a warning that “All existing apps and their data on the iPad will be replaced with apps from this iTunes library.”
I think my iTunes library is reasonably up to date (within a day or two prior to the format), and I also have my iPad connected to iCloud, although that doesn’t sync apps. What do I do in this case? Previously I had the option enabled, and apps that I purchased on the iPad transferred back automatically into iTunes whenever I plugged it in. I think all of the important apps are in my library, but what about the content of my apps on the iPad? For instance Pages has documents in it, will I lose these?
A: As scary as that warning message sounds, the good news is that you actually won’t lose anything as long as you still have all of the applications in question in your iTunes library.
These warnings for both apps and media content are somewhat common when you’re connecting to a new computer and/or new iTunes library, but can be a bit misleading; the implication is that iTunes will actually remove all of your existing content first, effectively wiping it from your device before syncing the content of your iTunes library back onto your device.
However, what iTunes actually does here is simply perform a comparison between what’s in your library and what’s on your device. In the process, it matches your device up with your selected content from your iTunes library, adding anything new, and removing anything that no longer exists or is no longer selected in iTunes. However, anything that’s already on your iPad that’s still available and selected in iTunes is left alone. This not only saves time by not recopying content that’s already there anyway, but in the case of apps ensures that your data is also left in place.
The catch here, of course, is that the apps must still be selected for synchronization to your device. If you enable the “Sync Apps” option with no apps selected, iTunes will go ahead and remove all of the apps on your device in order to match what you’ve selected (e.g. nothing).
So as long as you have the same apps available in your iTunes library and those apps are selected for synchronization to your iPad, everything should be fine. You can go ahead and choose “Sync Apps” from the dialog box—nothing actually happens here until you click “Apply” so you can then go through the list and make sure that all of the apps that are actually ON your device are still selected in iTunes. When you click the “Apply” button, iTunes will simply go through a sync process matching up what’s already there and leaving it alone, after which the “Sync Apps” option will remain enabled.
If you want to be extra cautious, you can always make an additional backup of your iPad in iTunes by right-clicking on your iPad in the Devices list and choosing “Back Up” from the context menu. This works for making a local iTunes backup even if you’re normally backing up your device to iCloud.
You can find that backup under Library/Application Support/MobileSync/Backup in your home folder if you wanted to make an extra copy of it just to be certain that it’s not overwritten by a later backup. This way, should you find that an app inadvertently gets removed and you lose critical data, you can simply put the backup back in places and use it restore your iPad along with the missing data.