you cant use the hard disk version to do anything that involves formating E:
Clean C partition install would be fine.
but you cant rebuild a disk...
and you cant use the clone hard disk function..
you should use the dvd version. its likley that you just need to burn Hexen to a dvd-r at 4x speed or slower.
The reason you cant use the hard disk version to format E is because thats where the hard disk version is..
The only reason i edited hexen to work from the hard disk was to let people with slimboxes / broken dvd drives, update theire Softmods, change dash, flash chips, run xbpartitioner, install a clean c:, or a few other usefull tools,
Thinking about it now some of the options should get dissabled from the hard disk version, every time some 1 mentions they will download it i have the horrible feeling they wont think that formating E will remove it.
I dont want to start messing to much with hexen though as it is not mine to play with. I only uploaded it so a few people could use it and in less than a week over a thousand coppies had been downloaded.