If you are doing an upgrade or restoring your iOS device such as iPhone then you will loose all the jailbreak applications that you might have installed on you jailbroken device. Although there is not any foolproof way to avoid this scenario but AptBackup can help to a lot of extent. Basically, this is a free application for the jailbroken devices that can be downloaded here from BigBoss repo. Once installed you just need to launch and press the Backup button to create a backup. After you loose your jailbreak applications say after doing a restore from iTunes you need to again download the application and launch it. Then just press the Restore to restore all the jailbreak applications.
Actually, this application stores a list of all the jailbreak applications in a text file on your iOS system and makes sure that this file is saved as well when you make a backup through the iTunes. This way this text file will also be restored when you restore the iOS device. This text file then tells the AptBackup on which applications to download. Only catch is that this will NOT restore the settings for the applications. Otherwise this application is quite convenient and can save you a lot of time to manually do the tedious process. Of course a jailbroken iOS device is required for this to work!
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