Restoring your device using iTunes will reinstate it. From what F0recast is saying, you have no SHSH blobs in Cydia, so you'll have to restore to iOS 7.0.4 if you want the setup.app back. Or, you'll need for someone to host their setup.app for the iPhone3,2 on iOS 6.1.2 or 6.1.3
The jailbroken iOS reindexes based on the available system data. If it's jailbroken, toggling any of the few resets will kill your device, forcing you to restore and rejailbreak.