AMAZING!
It worked perfectly! So, in case somebody needs it as well now that many have a second empeg, here are the few simple steps!

On the SOURCE Empeg
1) Install proper sw versions (Currently/Tested on Emplode 2.00b7 + HiJack 124)
2) Start your favorite ftp client (I used SmatrtFTP on WinXP) and enter the Empeg
3) Download the two direcotries Drive0 and Drive1, including all subdirs, to your local hdd.

On the DESTINATION Empeg
4) as 1)
5) as 2)
6) Send the custom command SITE RW to make the hdds writable
7) Copy the Drive1 and Drive2 directories from your PC HDD to your destination player, overwriting those in the DESTINATION Empeg
8) Send the custom command SITE RW to make the hdds read only
9) Wait 5 seconds at least that so that 8) is completed
10) Unplug and plug back your empeg.
DONE! Fids, Playlists, Dbase, all safe on your new unit!

What was not backed up with this method: EQualizer Settings, Time, Timecode, Date Settings. Maybe something else I did not notice yet.

A big big thank you to Mark Lord for such a great tool as HiJack!