If you've got the date command on your empeg then you could make it create a unique directory and then just recursively copy the entire CF card to the HD. That why you won't have any problems if the camera resets the file numbers for some reason.

#!/bin/sh
DIRECTORY = `date +%d%m%y-%k%M%S`
mkdir $DIRECTORY
cp --preserve --recursive /mnt/* $DIRECTORY

- Trevor