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I want to update my iPhone on iTunes but it says that it will delete all of the apps and media on my iPhone that I purchased. I synced it but I don't know what to do next. It says it will only save my content.

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Which version is currently on your iPhone, and to which version are you upgrading? I recall that 4 -> 5 required a backup and restore, but, having done the backup, I didn't lose anything. – Dan J Oct 22 '12 at 23:27

Make sure you have all your apps already loaded within your iTunes library. Then you can safely upgrade your iPhone via iTunes. At the end of the upgrade process iTunes will sync with your iPhone and will put back all your apps to your device.

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