I went thru itunes.
Was jb using with jailbreakme on 4 iphone 4s, downloaded pkgbackup and backed up all the cydia apps, backed up the current ios.
then updated and synced thru itunes
limera1n
loaded cydia, rebooted and redownloaded pkgbackup
restored thru pkgbackup
after pkgbackup my phones looked like the did prior to using limera1n, everthing was in its own folder, same pages, all my email accounts were restored even my exchange accounts.
did this for 4 iphone4s.
We are on ATT so baseband isnt an issue for us.
What version of itunes did u use?