There really should be an easier way to do this....
Wipe the handheld
Uninstall Handheld Software 4.0 from your PC
Uninstall Desktop Manager 4.0 from your PC
Install 3.x desktop and handheld software
Cradle the handheld and install 3.x on the handheld
Uninstall all the 3.x stuff
Reinstall all the 4.0 stuff
Reload 4.0 on your handheld
you now have a fresh version of 4.0
don't you feel like you accomplished something?