I'm not as smart as an Apple tech, and I can't explain why you can't see the backup you made prior to the upgrade, but here are a few thoughts.

I consider upgrading your iPhone from iTunes to be the normal and safe way to do an upgrade. This used to be the only option available before Apple implemented over the air updates a few versions ago. This is typically how I do an update. I've had to go through the restore to factory settings path and restore from a backup on my phone and my wife's, and other than taking a while, it was completely successful. I've also had problems on my iPhone after doing an over the air update that was resolved when I restored my phone, and I've seen reports on this and other lists, that others have had the same experience. I'm sure over the air updates are fine, and I've done them myself with smaller updates, but they do and will take more resources on your phone and thus in my opinion are more likely to lead to issues.

I assume you've tried powering off her phone and restarting it. I've seen my phone come up with the original factory look and feel after a restart, even when not updating my phone, and it was resolved by powering off and restarting my phone.

Note that your apps are not stored in the backup. To recover your apps, you need to let iTunes go through the process of syncing content (data and apps) to your phone. this will take a while, but it will copy the apps back onto your phone. The whole process of restoring to factory settings and restoring from a backup takes a while and goes through multiple steps. It should all just happen automatically, but it will take a while. Is it possible you interrupted the restore and sync before it was all complete?

Before I start an update through iTunes, I get a message that there are purchases on my iPhone which are not stored on my PC, and I need to go into the File pulldown to have these transferred. I'm sorry I don't recall the exact wording of this dialog, but did you see something similar and perform the requested step? I'm not sure if this has any bearing on what you're seeing or not.

In addition to performing a backup prior to an update, you also want to make sure your phone is synced with your PC/Mac, since there is data stored on your phone which will not be captured in your backup.

Note that as part of the update process through iTunes, a backup should be made, so again, I'm not sure why you aren't seeing this backup.

Finally, although you saw this problem performing an update through iTunes, there's no way of knowing if you would have seen the same issue performing the update over the air.

On 03/15/2014 12:03 AM, Alan Lemly wrote:
I realize in the world of computing most anything can happen a lot of
which is inexplicable. But my recent experience convincing a friend to
use iTunes to back up and upgrade to iOS 7.1 and the abysmal results
experienced have left a very bad taste in my mouth. The worst of it is
that the results we got seem to make no logical sense. Here are the
steps we followed:

 1. We backed up her iPhone 5 to her computer using an encrypted iTunes
    backup Wednesday night.
 2. Thursday night she started the upgrade to iOS 7.1 from within iTunes.
 3. Her phone was placed into recovery mode for some reason and had to
    be reset to factory defaults before the upgrade could proceed.
 4. The phone was upgraded and restored using the encrypted backup made
    Wednesday night but none of her apps were restored.
 5. We've determined to the best extent possible that the right backup
    was used for the restore but we are confused because the backups
    shown by iTunes under Edit, Preferences, and the Devices tab don't
    list any dated with Wednesday's date. I find this most perplexing
    because only one manual backup was made to her computer and that was
    Wednesday night.
 6. The iPhone Tech Support guy I spoke with tried explaining that if
    the backup was made to an unauthorized computer while using iTunes,
    the apps would not be backed up. We determined that her computer is
    authorized.

So, I convinced someone to use iTunes to upgrade her phone instead of
her doing it the normal way by running the upgrade from the General,
Software Update option as I expect most do. Now she's left with having
to re-download close to 100 apps and reconfigure them and re-download
any related content such as books, etc. And this comes at a time when
she is very busy and doesn't have the time to devote to it.

The final insult is that our results don't make logical sense. The
backup was encrypted to her computer using iTunes and she had to provide
the password before restoring. Everything I've read says that this is
the only way to get a complete backup of everything yet it did not work
as advertised for us. And I guess I'll be cured of my tendency to
attribute as operator error snafus posted by others since I know for a
fact that we did all the steps correctly but still got bitten badly.

I'm mainly posting this to help get closure with the incident but also
to warn others that you really can't be too careful backing up your
devices. And the next time you upgrade your iOS, you might consider
making an encrypted backup to your computer using iTunes but running the
upgrade from the phone.

Alan Lemly

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