I've never used it myself but try the Backup funtion.
Here's a quick cut and paste job from the EOS 4.0 Software Manual, it does say about backing up HD but I'm sure you can do it from CD Rom as it says you can select the SCSI drive.
To Backup your Hard Disk Data:
1. From the Disk Browser, select the SCSI drive you want to back up using
the cursor keys, INC/DEC keys or the Data Entry Control.
2. Press the Utils function key (F1).
3. Press the Backup function key (F5). The display will warn you if you are
about to overwrite the current bank in RAM.
4. Press OK to continue or Cancel to cancel the operation. The following
screen appears.
5. Select the destination drive using the INC/DEC keys, or Data Entry
Control.
6. Move the cursor down to ?Backup Type? and select the type of Backup
Type with the INC/DEC keys or Data Entry Control.