Just to be clear, the proper way to update to 6.1.2 is this:
1. Back up your phone to your computer (or iCloud if you prefer). If you want, also back up your Cydia stuff with something like PkgBackup (which makes the restore go faster).
2. Restore your phone in iTunes (this will wipe the device and update it to 6.1.2).
3. After the restore is complete, re-jailbreak with evasi0n.
4. Restore your iTunes backup. This will get you all your normal apps and data back. (or, if you really want, manually reinstall all your apps, but I've never had the inclination to do that).
5. Restore your Cydia tweaks, either manually or by a restore with PkgBackup.
I used PkgBackup, so the update to 6.1.2 took about 4 hours total, but I didn't have to interact with the phone very much. Just took about 1.5 hours to fully restore my phone (including syncing all my apps back), and then another 45 minutes to restore my PkgBackup data.