I tried that as well. It said: Clean is not allowed on the disk containing the current boot, system, pagefile, crashdump or hibernation volume. I don't understand how that is so if I'm booted on the other hard drive.
EDIT: I managed to use the cmd clean prompt by running my cmd before actual boot. This allowed me to wipe my secondary drive even with all the other errors I was previously getting while trying to do it during windows.