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open( P, "<", "Two.txt" ) or die "Two.txt: $!";
my @patches = sort <P>;
...
my $seq_num = 0;
$patch_id{$_} = $seq_num++ for ( @patches );

my %comp_patch;  # will be a hash of arrays
my $comp_name;   # will store most recently seen computer name
...
        $comp_name = $_;
    }
}

for my $cname ( sort keys %comp_patch ) {
    for my $pnum ( 0 .. $#patches ) {
...
            unless ( defined( $comp_patch{$cname}[$pnum] ));
    }
}