So this is the script so far:

#!/usr/local/bin/perl
use strict;
use warnings;
use Data::Dumper;
my ($key,$val);
open (FH1, "$ARGV[0]")or die("Error opening File1 $!\n");
my %hash1;
while(<FH1>){
            next if /(sample|value\d)/;         
            my ($key, $val1, $val2)= split /\s+/;
            push @{$hash1{$key}}, ($val1, $val2);   
            }
close FH1;

open(FH2, "$ARGV[1]")or die("Error opening File1 $!\n");
my %hash2;
while(<FH2>){
             next if /(sample|value\d)/;
             my($key, $val3)=split /\s+/;
             $hash2{$key}=$val3;
             }
close FH2;

my %hash3 = %hash1; 

foreach my $key2 ( keys %hash2 )
        {
        if( exists $hash3{$key2} )
                {
                push @{$hash3{$key2}}, ($hash2{$key2});
                                }
        else
                {
                delete $hash3{$key};
                
                }
        }

print Data::Dumper->Dump([\%hash1],['FIRST HASH']),"\n";
print Data::Dumper->Dump([\%hash2],['SECOND HASH']),"\n";
print Data::Dumper->Dump([\%hash3],['MERGED HASH']),"\n";
[download]

- It reads into hash correctly - It finds the duplicates and update the value array for duplicate keys - but it does not get rid of the unmatched keys and their values