use Fcntl qw(:DEFAULT :flock :seek);
my $old = "...";
my $new = "...";  # Assume it's safe to clobber this file.
my ($o_fh, $n_fh);
#
# The sysopen doesn't use the O_CREAT flag. If you the 
# task is to *change* $old, it should be an error if the 
# file doesn't exist.
#
sysopen($o_fh, $old, O_RDWR) or die "...";
flock($o_fh, LOCK_EX) or die "...";
# Now we have an exclusive lock.
#
# Open $new in read-write mode. Create if necessary.
#
sysopen($n_fh, $new, O_RDWR | O_CREAT) or die "...";
#
# Get rid of any existing data in the file.
#
truncate $n_fh, 0 or die "...";
while (<$o_fh>) {
    ...
    print $n_fh $_;
}
#
# Go back to beginning of files.
#
seek $n_fh, 0, SEEK_SET or die "...";
seek $o_fh, 0, SEEK_SET or die "...";
while (<$n_fh>) {
    print $o_fh $_;
}
#
# Truncate any remaining garbage.
#
truncate $o_fh, tell $o_fh or die "...";
close $o_fh or die "...";