It looks like you need something more like this:

#!/usr/local/bin/perl
use warnings;
use strict;

open MYFILE, '<', 'file.txt' or die "Cannot open file.txt: $!";

my %unique;
while ( <MYFILE> ) {
    chomp;
    next unless s/^(\d{4}-\d\d-\d\d)\s+\d\d:\d\d:\d\d\s+//;
    $unique{ "$_\t$1" }++;  # updated!
    }

print " - Found ($.)\n";
close MYFILE;

print "Remove duplicate lines\n";
print "Found (", scalar keys %unique, ")\n";

my @sorted = sort keys %unique;

print "format each line so that its formated as BulletinID,KBID,Title,
+Endpointname,Date\n";

my @sort;
for my $line ( @sorted ) {
    print "LINEPRINT - $line\n";
    push @sort, join "\t", ( split /\t/, $line )[ 2, 1, 3, 0, 4 ];
    }
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