I'm not sure I'm getting what your problem is. I transferred everything but radio station presents and eq settings from my old empeg (42Gb) to my new empeg (60Gb) by just:
1 - ftping ALL
from drv0 to g:\empeg-temporary-backup\drv0
and
from drv1 to g:\empeg-temporary-backup\drv1
(being G: one hdd in my PC)
2 - ftping ALL from
g:\empeg-temporary-backup\drv0 to drv0 on empeg
and
g:\empeg-temporary-backup\drv1 to drv1 on my empeg.

Used WindowsXP and SmartFTP.

That's all. Worked perfectly.

Hope this helps.