Q: We have an second-generation iPod touch and are running the current version of iTunes. We have just bought and downloaded three short films from the iTunes Store, each under 40MB. There is currently 3.87GB of space left on the iPod. After the purchase, we tried to sync them to the iPod and we got a this message: “Are you sure you want to remove all 73 applications from the iPod? This will delete these application and their data from the iPod.” We have enough room there; why would it want to delete the apps?
A: iTunes should never try to delete apps from your iPod touch unless you specifically ask it to. Even if your device is running low on space, iTunes will simply display an error message and refuse to transfer any additional content to your device; it will not remove content itself to make room.
If iTunes is suggesting that it’s going to remove applications from your iOS device it is likely because these applications have been removed from your iTunes library or de-selected for synchronization in your iTunes settings or you’re trying to synchronize your iPod touch to a different computer that does not have these apps installed. Check your Apps tab in iTunes to ensure that these apps are still in your library and haven’t been accidentally deleted, and also go to your iPod touch settings in iTunes and check the Apps tab to ensure that synchronization of Apps is still enabled and that all of the apps that should be on your iPod touch are still selected for synchronization.
If you have mistakenly deleted the apps from your iTunes library you can simply download them again from the iTunes Store at no charge. Once they are back in your library they should automatically match up with the apps already on your device.