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I tried upgrading to an iPhone 4s. After starting the phone, I chose to restore from iTunes and it told me to connect via USB, which I did. It went through what appeared to be a normal sync process, but after doing so, only my photos appear to have synced to the phone. There were 0 apps and 0 songs and 53.6GB Available through the About screen on my phone.

The default apps as well as any Safari Home Screen links all were there as well as the config of my favorites and a few of the folders (the ones which contained default apps).

I've tried resyncing a few times as well as doing a Restore, but I can't get any apps or music from my MacBookPro.

I noticed one thing about my apps. They overflowed the 11 screens as they pulled them out of folders. I tried to clear that up to no avail.

I've also restarted iTunes, the phone and the Mac.

The capacity bar when I have my phone plugged in lists 117 apps and 1500+ songs, none of which will sync. I grabbed an app directly from the App Store on my phone to see if it would sync back to the Mac, but it did not. Both phone and iTunes are using the same account.

Any suggestions? Any way to troubleshoot/logs to look at (I found nothing of interest in /var/log and did not find any log files that iTunes was writing to)? I really don't want to start adding from scratch as I want to keep my state and data.

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Restore your phone again. Plug it in, in iTunes press Restore from Backup, and select the backup from before you started the iOS5 update. –  Hand-E-Food Oct 16 '11 at 22:10
    
Restored several times, both from iTunes and after doing a wipe on the phone. –  Tim Oct 18 '11 at 23:00

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