Sometimes you have to remove the current options in order to manipulate the selected options.
Here is an example how to set options:
<select id="mySelectId" class="chosen-select" multiple="multiple">
<option value=""></option>
<option value="Argentina">Argentina</option>
<option value="Germany">Germany</option>
<option value="Greece">Greece</option>
<option value="Japan">Japan</option>
<option value="Thailand">Thailand</option>
</select>
<script>
activateChosen($('body'));
selectChosenOptions($('#mySelectId'), ['Argentina', 'Germany']);
function activateChosen($container, param) {
param = param || {};
$container.find('.chosen-select:visible').chosen(param);
$container.find('.chosen-select').trigger("chosen:updated");
}
function selectChosenOptions($select, values) {
$select.val(null); //delete current options
$select.val(values); //add new options
$select.trigger('chosen:updated');
}
</script>
JSFiddle (including howto append options): https://jsfiddle.net/59x3m6op/1/