The following is the solution if you are getting the corrupt backup error during a sync or backup in iTunes (during a sync, the sync is just triggering a backup):
During a sync or backup, deleting the backup is the way to go, and iTunes will create a new one from scratch. However, the original poster has the additional issue that the backup isn't appearing in iTunes.
@doncherry has the correct idea -- if iTunes isn't listing your backup in the Preferences->Devices list, then you need to delete the backup manually. He has pointed out the location to look in Windows. On a Mac, the backups are stored in
/Users/<your username>/Library/Application Support/MobileSync/Backup
Open Finder, (hold the option key on OSX Lion or higher), and select
Library from the
Go menu. This will open the
Application Support folder, and from there, go to
Backup. In the backup folder, there will be one or more folders named by your devices' unique identifiers.
In iTunes, click on the
Serial Number in the Info tab for your device, and the
Serial Number field will switch to your device identifier. Match the identifier you see there to a folder name in the
MobileSync -> Backup folder. Delete that folder!
If you are getting the corrupt backup error during a restore in iTunes, clearly deleting the backup isn't going to help you get your data restored ;)!
I'm the lead developer on a program called Decipher Backup Repair, which is why I know and care so much about iTunes backup and restore errors ;) Decipher Backup Repair will scan your corrupt or damaged iPhone, iPad, or iPod Touch backup for errors and fix the problems in the backup so you can restore in iTunes. You can download the free trial from our website to see what it can find in your backup.
(Clearly, I stand to benefit from the links I am posting in this answer, as the author of the software. However, I wanted to give both sides of the issue, corrupted backups during the backup process, and corrupted backups during the restore process. Anyone is also welcome to follow the links above and navigate to our support page to send us an email if you have questions about your corrupted backup. Feel free to mention my name directly: Kelly.)