From >4.0 in order to really clean the select2 you need to do the following:
$remote.select2.val('');
$remote.select2.html('');
selectedValues = []; // if you have some variable where you store the values
$remote.select2.trigger("change");
Please note that we select the select2 based on the initial question. In your case most probably you will select the select2 in a different way.
Hope it helps.