#!/usr/bin/perl

use strict;
use warnings;
use Data::Dumper qw/Dumper/;

my @pairs_in_db = ([1,2],[1,9],[3,4],[5,6]);
my @pairs_from_somewhere_else = ([1,2],[5,6],[7,18]);
my @pairs_to_delete=@pairs_in_db;

my @pairs_to_create;


NEW:
for my $new (@pairs_from_somewhere_else) {
  for my $old (@pairs_to_delete) {
    if (defined($old) and "@$new" eq "@$old" ) {
      $old=undef;
      next NEW;
    }
  }
  push @pairs_to_create,$new;
}

print Dumper \@pairs_to_create,\@pairs_to_delete;