You code did not duplicate the data. Propably you did not show the important part. However, you should use strict and use warnings;. Check open for errors and propably use binmode on your filehandles. Here is a cleaned version from your code. Untested... Ups, add the flocks.

use strict;
use warnings;
use CGI qw/:standard/;
use Fcntl ':flock';

my ( @dataWrite, @dataRead );

open( my $in, "<", "../Rules1.txt" ) or die $!;
binmode $in;
flock($in, LOCK_SH);
@dataWrite = @dataRead = <$in>;
flock($in, LOCK_UN);
close $in;

push @dataWrite, "Code1\n";

open( my $out, ">", "../Rules1.txt" ) or dienice("Can't open counter.t
+xt: $!");
binmode $out;
flock($out,LOCK_EX);
print $out @dataWrite;
flock($out,LOCK_UN);
close $out;

print "Content-type: text/html\n";
print("\n");
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