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After backing up my iPhone 3GS and then updating to the new iOS 5.1.1, I lost all my apps and saved notes/data. How can I get all the apps back?

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From which version did you start the update? Some jumps actually erase the phone and then depend on the backup to restore things. It's hard to tell what may have happened, but it's clear that something failed since an erase isn't the intent of an upgrade. Before you go further - be sure you don't overwrite your backup with a new empty one by renaming the phone or checking your computer back up is itself backed up as iTunes only keeps one backup per device most of the time. –  bmike Jun 8 '12 at 16:53
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When I first updated to iOS5 I lost all of my apps too. Interestingly, it had the spinning sync icon at the top of the phone for a few hours after as it manually downloaded all of the apps. They suddenly appeared one after another. Perhaps it's doing this.

Try downloading an app that you had and see if it still has the settings/saves it had. If so, I'd expect this is the case.

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Thank you Kalamane, but I did the backup through iTunes. Under "Backup" there was an option for "Encrypt local backup." After this and the update, it only backed up my photos, contacts, and text messages but none of the apps. Is there any way to get the apps back? –  Firstime69 Jun 8 '12 at 16:34
    
I've updated my answer to reflect this. –  Kalamane Jun 8 '12 at 16:39
    
@ bmike: I used iTunes 10.6 –  Firstime69 Jun 8 '12 at 17:14
    
I noticed that as well when downloading the same apps again, that their data was saved, but the apps haven't reappeared yet. Does this have anything to do with jailbroken apps? If i had previous apps that were jailbroken, would they be lost and unable to get back? –  Firstime69 Jun 8 '12 at 17:17
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