ok, here is a start: untested

#!/usr/bin/perl
my $dir = shift or die "need a directory name";
opendir my $fd, $dir or die $!;
for ( readdir $fd ) {
  next unless /\.AU~$/;
  my $old = "$dir/$_";
  next unless -f $old;
  ( my $new = $old ) =~ s/~$/W/;
  rename $old => $new unless -e $new;
}
closedir $fd; #thx fletch
[download]