You cannot and never could with updating the firmware and maintaining all packages and the JB untouched.
Either way you will have to reinstall them. Either one by one or using a batch installer all at once like mentioned above.
1). Backup your phone (both with iTunes and PkgBackup)
2). You restore your phone to 6.1.2 stock (unjailbroken).
3). Jailbreak using Evasi0n 1.4 (when available later today).
4). Restore your iTunes backup
5). Restore your Cydia packages with PkgBackup
Anyone else having trouble getting pkgbackup to backup to Dropbox? Mine fails after trying 10 times. Not sure what the problem is but I'm going to log out of my dropbox and log back in. Will report back with results.
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Didn't work. Can someone else please try and let us know if it works for you?