I am thinking about upgrading my jailbroken firmware from 3.01 to 3.12. I never done this before on an iphone however I have jailbroken many times on my ipod touch. I was thinking about using this method for my 3gs http://www.ihackintosh.com/2009/11/jailbreak-unlock-iphone-3g-3gs-3-1-2-with-blackra1n/ When I use this method, what can I expect to be missing after the upgraded jailbreak? I am trying to keep all of my settings and applications unchanged. Is this possible. I think that the cydia apps will be gone and I heard that there is an app that keeps track of the cydia packages that I downloaded and it will redownload them after the update and I heard that all of the settings for those apps that I had previously will be gone. Will all of the apps that I got from the app store still be there and the settings intact? I do have one app that I downloaded from [PIRACY]us but it is a free app that can be downloaded from the app store. The only reason why I downloaded it from [PIRACY]us was I liked an older version of the free app and I could not find it anywhere else. This should not be considered piracy. Anyway, I have been using that app for awhile. I have a lot of settings and time put in using that app. I am worried that since I did not download it from the app store, the app and my work will be lost during the upgrade. Will this app remain intact? Which kind of applications and settings will be gone if I upgrade the firmware? Are there any more steps that I can take to back up everything. Can I use WinSCP or SSH in with putty and backup entire files and directories and try to restore them afterwords or would that create some problems?