I may be a little late with this, but I have been programming for over 30 years and "flush" is always used to clear the input buffer of any remaining characters. Why has it been changed in 1.0??
It depends on the context, in output contexts, flush means make sure all characters that are queued up to be written are indeed written out, i.e. fflush in the C standard I/O library.
BTW, in the Suggestions for the Arduino project
forum, you would have seen a discussion in the last 2 days on the same topic, including a post from the guy who made the change: http://arduino.cc/forum/index.php/topic,116602.0.html