Maybe try searching online for the main issue. This is the first I've heard of the issue. You could just write down the apps that you need to reinstall. Usually PKGBackup saves all from Cydia.Neither worked. Do I really have to do another restore and jailbreak? I had to install several Cydia apps that did not save with PKGBackup.
Your best bet is restore and re jailbreak to see If it was just a bad jailbreak.