I have read many tutorials on how to upgrade my 3.1.2 firmware to the new iOS4 for my already jailbroken 3GS iphone (old bootrom, Blackra1n jailbreak). All of them explain how to backup the list of apps installed from Cydia (using APTBackup in example) so you can recover them easily after the firmware upgrade. But none explains what happens to the other apps (such as games) that have been installed manually from downloaded IPAs, as well as the files that are created by those apps for customization or saves. I am a big tester and my iphone carries more than 100 manually installed apps. Therefore I am considering not to upgrade my firmware if that means I have to install all of them again manually. Can anybody tell me what happens to those (hacked) apps when upgrading to a new firmware ? If the firmware upgrade involves the re-installation of all my apps, what would be the easiest way to do it, so I don't spend a full night or weekend on the process ? FYI, I use WinSCP to transfer IPAs from my PC to the 3GS, and then Installous for setup. Thanks for your help.