I am having the same problem.
Although I will admit that I am a n00b (not really new, just inexperienced, i'm in IT and can have a basic understanding of what is going on in a modded box) and a bit of a Kamikaze.
I did not build my box, it came to me with a Xenium (version?) and X2 (again, version?), I decided to throw caution to the wind and upgrade the Xenium OS from 1.0 ro 2.01.
Following the tutorial
Xbox-Scene Tutorial: Newbie guide to installing Xenium and EvolutionX (v0.1)I flashed from 1.0 to 1.1, no prob. Washed, rinsed, repeated to v2.01
Then I had to find a bios. I can't say which X2 build I finally went with, but suffice it to say I was finally able to boot into my UnleashX dash. But when I navigated to my Games, it came up empty, same with my Emulators and recorded music (both housed on my F: drive).
When I FTP through the Xenium OS I can see everything on the F drive (much to my relief, I once inadvertently formatted all my Xbox drives, that would be the Kamikaze coming out). But when I FTP through the dash (bios), I see nothing. The F drive shows, just nothing there, and no space available.
Take it one step further, I deleted off some stuff from F, lo and behold now I was showing free space (not as much as there should have been, before the upgrade I had about 3.5 gb avail, now only what I had deleted). I reloaded one of the deleted items and BAM! it now shows from within the dash.
Is there a way to migrate these files and directories without offloading everything, formatting, and then reloading it all (around 120gb)?