Okay. Here is the code I came up with attempting to implement your suggestion and anon's. I will adopt for the real deal shortly and post soon.

HEADER
a1
a2
a3
a4
a5
a6
a7
a8
a9
a10
END HEADER
b1
b2
c1
c2
..
z1
z2
[download]

I chose a5 as the line to change and want to only change that line, everything should be exactly the same.

#!/usr/bin/env perl
use strict;
use warnings;
use Data::Dump;

open (my $fh, 'message.txt') or die $!;

LINE: while (<$fh>) {
   last LINE if /END HEADER\s\w/s;
}

my $headerEndingPositionInBytes = tell($fh);

print "Found header ending at $headerEndingPositionInBytes\n";
sysseek $fh,0,0; # Rewind to beginning of file

my $header;
my $bytesRead = sysread $fh, $header, $headerEndingPositionInBytes;

print "Read $bytesRead into header variable\n";

my @lines = split '\n', $header;
for (0..$#lines) {
   $lines[$_] =~ s/^a5$/new magic/;
}
$header = join "\n",@lines;

open (my $newFile, '>','message-fixed.txt') or die "$!";
syswrite($newFile, $header); # Write the header


my $blockSize = 32 * 1<<10; #32k
my $window;
while (my $bytesRead = sysread $fh, $window,$blockSize) {
   syswrite $newFile, $window, $blockSize;
}
syswrite $newFile, "\n";
[download]