Nothing special. Just the normal unix "cp" command running directly on the empeg to copy one hard drive device to the other. Once it's done, I'll adjust the last partition boundary to take advantage of the ~2 extra gigs the CF card has over the old spinning disk. Cloning the second disk to the second CF card might be a little more hairy, as thats the disk that was starting to fail. It seems to be a spinup issue though, and once it's up, it remained stable for a number of days.

Since I'm in no rush, and I lack easy access to a machine with IDE, this was the easiest method for me.