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my %combined;
open(my $input, "<", "flatfile.dat") or die ("Unable to open file");
my $line = <$input>;
...
        push( @{ $combined{$header} }, shift(@row) );
    }
}

#Remove duplicates
my %seen = ();
my @uniqueOutput = grep { ! $seen{ $_ }++ } @output;
print $fh3 @uniqueOutput;