entityQuery array instead of orConditionGroup()
I don't know how it was working before, but the solution seems to be to place the explicit 'IN' in the query as such:

$results = \Drupal::entityQuery('node')
  -&gt;condition('type', 'mytype')
  -&gt;condition('status', 1)
  -&gt;condition('field_first.target_id', $anArrayOfNids, 'IN')
  -&gt;condition('field_seciond.target_id', array($anotherNid))
  -&gt;execute();


Or, if I was to just convert this to the more complicated, yet more robust method:

$results = \Drupal::entityQuery('node');
$group = $query-&gt;orConditionGroup();
foreach($anArrayOfNids as $nid) {
  $group-&gt;condition(field_first.target_id, array($nid));
}
$query-&gt;condition('type', 'mytype')
  -&gt;condition('status', 1)
  -&gt;condition('field_seciond.target_id', array($anotherNid))
  -&gt;condition($group)
  -&gt;execute();