How to save values on each form submit without overriding saved datas?
Config items can be arrays, so something like this should work. (Note that I haven't actually set it up to try it).

      $new_filter = $form_state-&gt;getValue('ldap_filter');
      $filters = \Drupal::configFactory()-&gt;getEditable('amu_import_ldap.settings')
        -&gt;get('ldap_filter');
      $filters[] = $new_filter;
      \Drupal::configFactory()-&gt;getEditable('amu_import_ldap.settings')
        -&gt;set('ldap_filter', $filters)
        -&gt;save();


Of course that's a very naive example, you may wish to check you are only adding unique items to the array, and so on.