but, sorry . . . its obvious the if you boot from the Emergrncy disk, the snapshop done under an HD AmigaOS installation, will go lost.
Start the system from the EmergencyDisk and then snapshot the icons from there. (take the Emergency Disk writable)
There are other reason for this behaviour (ie some hidden partition set with Workbench Prefs)
EDIT- when you say "i boot from EmergencyDisk", you mean with the EmergencyDisk+CDROM? . . . even worse. You can't.