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I updated my iPod to iOS 5 and all my apps and their save files are missing. I backed them up to my computer but can not find them.
How do I restore the backup?
Backups are managed by iTunes, there's no need for you to know where the actual files are (This is the beauty about Apple things).
To restore your backup connect your iPad, right click it in iTunes' sidebar and select restore from backup (Sometimes it helps to restore from backup twice).