This should be fairly simply if you save the items selected. For example:
<select data-placeholder="Choose a country..." style="width:350px;" multiple="true" class="chosen-select">
$(".chosen-select").chosen();
Now, before updating the chosen, make sure you save the items selected like this:
var chosenSelectedItems = $(".chosen-select").val(); // this gets you the select value data
// Update the select items
$('.chosen-select').trigger('liszt:updated');
$(".chosen-select").val(chosenSelectedItems);
This should be able to reset the original values before the change.
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