You will have to use an app saver to do that.
Or, if you have Nova Launcher installed, it will save the home pages and folders. Nova launcher is kind of neat in that you can send the backup to yourself via email as the backup is created. That is the only way I use it. The home pages, not the apps.
Kies 3.0 just saves the basic app and phone settings.
Been there, done that, and also much frustrated when it happened.
Helium can be used to store apps, but I like "My Backup" better for that.
but with all backup programs, if you don't pull the backup file off the phone and store it on your pc, in the cloud, then the backup is lost right along with the phone when it is Factory Reset.