Most common problem is that people are trying to run these command from terminal manually and not by logging in with ssh. In that case any typo or perl command will mess up your refhashlist. To recover you need to check what sha1sum line differs in refhashlist, and fix the line and resign.

That disclaimer is there for a reason, if people dont login with ssh and use copy paste, you most likely end up in brick and need to reflash.