IPhone – How to extract photos from iPhone backup files

I don't have a great answer - but this is fairly serious so I'm going to start an answer and hope someone else edits or answers if they can spot something I haven't.

On the computer, the only "red flag" would be if you wiped the phone of all content and settings, named it exactly the same name as it was before (which could be iPhone) and then backed up again and overwrote the backup with the actual data. iTunes tries hard to prevent this and spawn off a date-protected backup when it detects this, but I've seen this check fail and people lose backups from time to time. The remedy here is to restore the PC from a backup that has whatever MobileSync folder is the most recent.

On iCloud - you also shouldn't be able to overwrite a "full" backup with an empty one. Also, iCloud explicitly keeps several versions of the backups going back in roughly day intervals. It also normally stores backups for different devices without collisions or overwriting another backup.

The good news on iCloud is you can always get help from Apple at http://www.apple.com/support/icloud/ and from retail stores. New devices or ones covered by Apple Care also have phone or web support in most countries. All new Apple products have a 90 day window of set up help. Hopefully one of these can step in and assist. Not only does Apple get a data point where their tools let you down (and exactly what circumstances this happened) - they also see many people in this situation and will hopefully waste a minimum of your time getting this sorted.

I have restored plenty of iOS 5 backups onto iOS 6 devices so the problem here is almost certainly that the backup is now (and may have been all along) corrupt.

Before throwing that backup away and restoring the iTunes files from a backup of the computer where it was stored (hopefully you have that), you could try restoring the backup onto another device such as a borrowed iPad or iPod touch (or iPhone) to be sure it's not the phone you are restoring the backup to.

The article iTunes: About iOS backups will help you locate where your computer stored this backup set as well as general info to support the idea that you can back up an older OS onto a newer OS (but not the other way around).