Yeah...I know it is a pain. I thought this release was going to have the capability of saving folder configuration. I guess not. Wiping the partitions wipes everything...don't accidentally wipe your SD card tho.
NEVERMIND!!! Reading back in the forum under Saving Screen Layouts...? by Corman324.
It says to use Miui Backup/System for the screen layout backup. I just tested it and... low and behold it works. Oh happy day!!!