You have a couple of problems...
1) To identify the secondary rows, in custom.js, change this line:
Code:
secondaryRows.css({ 'margin-left':'2.5em' });
To this:
Code:
secondaryRows.addClass('secondary-item').css({ 'margin-left':'2.5em' });
2) You have somehow moved both answers lists into the same question so trying to identify items by question ID won't work. Use this as the "un-checking" script:
Code:
<script type="text/javascript" charset="utf-8">
$(document).on('ready pjax:scriptcomplete',function() {
// Add classes and attributes
$('li.question-item').closest('ul').addClass('inserted-question-list');
$('li.question-item').each(function(i) {
$(this).attr('data-index', $(this).index());
});
$('body').on('change', '.secondary-item input:checkbox', function(i) {
if($(this).is(':checked')) {
// Identify some stuff...
var thisQuestion = $(this).closest('.multiple-opt');
var thisList = $(this).closest('ul.inserted-question-list');
var otherList = $('.inserted-question-list', thisQuestion).not(thisList).first();
var thisIndex = $(this).closest('li').attr('data-index');
var otherItem = $('li[data-index="'+thisIndex+'"]', otherList);
// Uncheck the check-box in the other question
$('input:checkbox', otherItem).prop('checked', false).trigger('change');
$('input:hidden', otherItem).val('');
}
});
});
</script>
Sample survey and theme attached: