Updating doesn't delete anything or undo anything, except for system files (flashcardtimewarp/mset).
Why is it so hard for you to just reinstall FBI or whatever after formatting? Use GW launcher to format emunand then everything on your current sysnand will be saved to emunand. Then you can update emunand any way you want, and remove the SD card, format sysnand through system settings, then put the SD card back in and reinstall the cia installer the same way you did it the first time.
Edit: oh, and don't forget to backup everything on the memory card first, before formatting emunand. OR if you already have an emunand, just dump your NAND through the GW menu and inject it to emunand with emunand tool.