This is just a backup in case something goes wrong during the normal backup/upgrade/restore process or if the device unexpectedly won't boot and has to be reloaded. There may be a few apps that this method doesn't pick up. However, if you are doing an OS upgrade, Desktop Manager should show all the apps installed on the device and backup and restore everything. There are a few apps where some of the data doesn't restore however. CryptMagic has it's own database on the PC that you can restore back to the device.