Sorry, I can't provide the full data due to that pesky confidentiality stuff, and I know that's not very helpful. Hopefully this will be just as good. Here is the same code tweaked a little to be more stand alone.

#!/usr/bin/perl
use utf8; use 5.022; use strict;

# Open the file for input, discard all the header lines, but stop on a
+nd save the column names in an array.
# Then read all the remaining lines in to an array and close the file.
my $filename = "test.txt";
my $fh;
open($fh, "<", $filename) or die "Cannot open \"$filename\" for input:
+ $!\n";
my $column_line = "";
$column_line = <$fh> while !($column_line =~ /Invoice ID/i);
chomp(my @columns = split /\t/, $column_line);
chomp(my @data_lines = <$fh>);
close $fh;

# Sort the data lines according to the "Company Name" field, and then 
+the "Invoice ID" field.
my ($company_name_index) = grep { $columns[$_] eq "Company Name" } (0.
+.$#columns);
my ($invoice_ID_index) = grep { $columns[$_] eq "Invoice ID" } (0..$#c
+olumns);
@data_lines = sort
{
    my($company_name_a, $invoice_ID_a) = (split /\t/, $a)[$company_nam
+e_index, $invoice_ID_index];
    my($company_name_b, $invoice_ID_b) = (split /\t/, $b)[$company_nam
+e_index, $invoice_ID_index];
    fc($company_name_a) cmp fc($company_name_b) or
    $invoice_ID_a <=> $invoice_ID_b
} @data_lines;

# Open the file for output, print the standard header to it, print the
+ now sorted data to it, then close the file.
open($fh, ">", $filename) or die "Cannot open \"$filename\" for output
+: $!\n";
print $fh "Replacement Header Text Here\n\n$column_line";
print $fh "$_\n" foreach @data_lines;
[download]

And when I run that with the exact original contents of the "test.txt" file as follows:

Original Header Text    
    
Invoice ID    Company Name
1    SEBASTIAN COMMUNICATIONS
2    MASQUE SOUND
3    SEALEVEL SYSTEMS
4    MASSTECH, INC
5    SE INTERNATIONAL
6    SOUTHEAST SERVO, LLC
7    SEALEVEL SYSTEMS, INC.
8    MASTERBILT
[download]

Then the resulting modified "test.txt" file is:

Replacement Header Text Here    
    
Invoice ID    Company Name
4    MASSTECH, INC
7    SEALEVEL SYSTEMS, INC.
6    SOUTHEAST SERVO, LLC
2    MASQUE SOUND
8    MASTERBILT
5    SE INTERNATIONAL
3    SEALEVEL SYSTEMS
1    SEBASTIAN COMMUNICATIONS
[download]

Does that help? Or rather, help you help me?