The Drive Upgrade Guide has instructions on how to clone the data from one drive directly to another, when both are plugged into the empeg. It's under "Step 7: Copying files (special circumstances only)". Make sure the new drive is fully built and formatted and has freah player software on it before doing that.

If you don't want to open up the empeg to do the job, you can do it using some of the backup and restore tricks listed here and/or here.