Alex, you should also mention that iRex says NOT to use the companion software to back up the iLiad. Apparently when you hook your now empty iLiad back up to the companion software it deletes everything you backed up since it is now missing from the iLiad!
BTW their 2.9.5 er_registry.txt upgrade script also seems to not have been well crafted either. If you have updated your er_registry.txt then you need to be VERY CAREFUL about applying this update. In fact you might want to go back to a backup of your original er_registry.txt prior to the upgrade.
Otherwise you may be waiting for them to release their CF flasher (or sending your iLiad back for a reflash.)