When I went from IOS 3 JB to 4.21 all my JB apps were still there they just wouldn't run till I jail-broke the ipad again. Then they all ran and I did not have to reinstall anything other than re-jailbreak.
Now I want to update from 4.2.1 to 5.1.1 but things seem different. The update says that itunes will backup and restore the apps itunes knows about inferring that the JB apps will not be restored. Does that mean that they will be gone? Or will they still show up on the desktop and not run until the ipad is jailbroken again or are things different now and these JB apps will be completely gone or still there as before?