I recently upgraded my 4.3.1 jailbreak to 4.3.2 using sn0wbreeze. Several people have asked for a rundown of the process, and it should be applicable to upgrading any version of JB iOS to any other version (including the same version number):
Personally I use PkgBackup (a paid app in Cydia) to ensure I can backup and restore my JB configuration when doing minor OS upgrades. There are other free solutions which may work for you. I also use DropBox for backup storage as it is free and convenient.
The premise of this approach is that you want your Jailbroken iPad to be exactly the same at the end of the restore as it was at the beginning, except with an upgraded IOS.
The following twelve step procedure was used to achieve the upgrade:
1. Perform PkgBackup backup onto DropBox for all JB apps, settings & repos - This is as simple as pressing the "Backup" button in PkgBackup (once you have provided your details and configured your backup options - use the "cog" button in PkgBackup to set these).
2. Perform full iTunes Synchronisation to backup all iTunes apps, settings, & media sync settings.
3. Create and install a sn0wbreeze custom firmware - The full tutorial is available here. Using sn0wbreeze is the easiest approach for an upgrade in my opinion, however...
...you could also put your device into DFU Mode (http://www.ipadforums.net/ipad-hacki...e-dummies.html) and restore the iOS version you are moving to using iTunes. Then follow either our redsn0w tutorial (http://www.ipadforums.net/jailbreaki...w-windows.html) or visit jailbreakme.com if you device and version of IOS is suitable for this method - The end result just needs to be the same. Once you have finished you should have a clean iPad freshly jailbroken with Cydia on it!
4. Once freshly jailbroken, disconnect the iPad and connect to your wifi network (if applicable).
5. Open Cydia and install PkgBackup as the first package (also installs several dependant packages).
6. Reboot iPad.
7. Open PkgBackup and configure to connect to DropBox and switch to the "View Restore" tab.
8. Perform full restore from backup made in step 1 using PkgBackup. Sometimes, for particularly complex setups, you may need to reboot and run the exact same restore operation again to get all packages restored. This is due to a limitation in the way some package dependencies resolve in complex setups.
9. Reboot iPad and connect to iTunes.
10. Select 'Restore iPad from previous backup of' option when prompted and ensure the backup you made in step 2 is selected.
11. Allow the restore to complete and your iPad to reboot – do not disconnect from iTunes.
12. Once rebooted and reconnected to iTunes, press the “Sync” button to synchronise all your Apps and Media back to the iPad.
At the end of this process you should have a jailbroken iPad with precisely the same configuration as you started with, but on the new operating system.
All in all this process took around 2.5 hours, however the vast majority of this (2 hours) was step 12 which is re-syncing 50GB+ of media to my iPad. If you plan the process well the iPad can be left unattended at this stage and you can go off and do something more interesting until it completes!
Hope this helps others understand the process I went through.