mine is just as modded to death as it was before, backup is your friend
i use winscp to back up the usr/share folder so i can reapply all my mods and icons and stuff, and the backup program will reinstall all your programs and settings for you, and i copy the whole N900 folder to pc too, does take about 3 hours transferring it all back but most of that time is spent transferring music and video through the data cable
but it does give you a very nice clean update