Hi,
xbmc and dvd2xbox are applications you can run on your xbox due to the softmod. You can ftp those back to your xbox harddisk when the softmod is running. (You can use xbmc as your dashboard as well.)
The important parts are the C and E partition of your xbox harddisk.
Xboxhdm can prepare a xbox disk. It will copy everything that is in it's C and E folder to the C and E partition of that disk.
So, you should put the contents of your real C and your E of your current xbox disk in there. Than, you can recreate the xboxhdm bootcd iso and burn it to a cd. With that cd, you can prepare your harddisk.
So, it is important that you use your real C contents and not those of your shadowc. As your shadowc is normally a file on your real c, it's contents will be copied over as well.
regards.