Do You Lose Your Apps When You Jailbreak an iPhone?by Aaron Parson
Jailbreaking an iPhone, despite voiding your warranty, will not prevent you from continuing to use all the apps you've bought through the iTunes App Store. Rather, the process adds an alternative app store, Cydia, to your phone, which works alongside the official App Store. Though jailbreaking itself will not remove your old apps, the process may occasionally require you to restore the phone's operating system, forcing you to recover your apps from a backup or to re-download them.
Normal Jailbreaking Process
When you run a jailbreaking utility on your computer, the software will send various commands to your phone. During this process, your phone may reboot several times. After the jailbreak finishes, your phone should still have all your old apps on it, plus the Cydia app. You can download apps and system tweaks from Cydia while continuing to shop for apps from the iTunes App Store.
Even after jailbreaking, you can continue to sync with iTunes on your computer. The sync process will not alter or remove your App Store apps, nor your Cydia apps. In some cases, however, tweaks from Cydia may cause apps to appear improperly on iTunes. For example, if you hide apps on your phone using a jailbreak tweak, they will still appear on iTunes on your computer. Despite the inconsistency, syncing will work correctly.
Both jailbreaking itself and installing apps from Cydia carry some risk of corrupting your phone's system. If this happens, you will need to restore the phone using iTunes. While you will never lose access to your purchased apps -- you can always redownload apps you've paid for -- this process will erase your app data, restoring it to the date of your last sync. To avoid data loss, always sync your phone before jailbreaking or testing out new jailbreak apps.
Losing Cydia Apps
While jailbreaking will not remove App Store apps, updating your phone's system, restoring it or re-jailbreaking will remove all apps downloaded from Cydia. After a new jailbreak, you will have to download all such apps again. Paid apps remain tied to your Cydia account, so you don't have to pay again. You can also install the Cydia backup apps such as PKGBackup or xBackup to back up and restore your Cydia apps all at once.