I don't know exactly where your problem is; but if I had to do that, I might write it like this, using a module to parse the CSV:

use IO::File;
my %old =
    map { $_->[1] => $_->[0] }
    map { chomp; [ split /,\s*/ ] }
    IO::File->new("<$file_old")->getlines;

use Tie::Handle::CSV;
my %new =
    map { ( $_->{'CN'} => $_ ) }
    map { { map { /(.*)=(.*)/ } split /\.(?=[A-Z]+=)/, $_->[3] } }
    Tie::Handle::CSV->new($file_new,header=>0)->getlines;

# now %old and %new are keyed by PC ID.
# you can use the standard techniques for finding keys that
# are in one but not the other, e.g.

my @new_PCs = grep { not exists $old{$_} } sort keys %new;
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