You would have to restore first, then rejailbreak. You will lose all your jailbroken apps if you do not back them up. I'm sure you know how to backup the regular parts of the phone through iTunes, but as for 3rd party apps like from Cydia, you will lose them.
I suggest using AptBackup (not APPbackup) or if you have a buck or 2 to spare, buy PkgBckup. It's supposed to be more stable.