$(hiddenInput).attr('checked', checkedState);

$(hiddenInput).prop('checked', checkedState);

<script type="text/javascript" charset="utf-8">  
  $(document).ready(function() { 
 
    // Call the function
    countChecked('{SGQ}');
 
    function countChecked(sgq) {
      // Identify the questions
      var sID = sgq.split('X')[0];
      var gID = sgq.split('X')[1];
      var qHiddenID = sgq.split('X')[2];
      var qHidden = $('#question'+qHiddenID+'');
      if($(qHidden).length > 0) {
        var q1 = $(qHidden).prevAll('.array-flexible-row:eq(0)'); 
        var q1ID = $(q1).attr('id').split('question')[1];
        var q2 = $(qHidden).nextAll('.array-flexible-row:eq(0)'); 
        var q2ID = $(q2).attr('id').split('question')[1];
      }
 
      // Hide the hidden question
      $('#question'+qHiddenID+'').hide();
 
      // Assign column-specific classes to Q1
      $('.answers-list', q1).each(function(i){
        $('td.answer-item', this).each(function(i){
          $(this).addClass('answer-column-'+(i+1)+'');
        });
      });
 
      // A listener on the 1st column of Q1 radio buttons 
      $('.answer-column-1, .answer-column-2', q1).click(function () { 
        handleHiddenInput (this, 'checked');
      });
 
      // A listener on the 2nd and 3rd columns of Q1 radio buttons 
      $('.answer-column-3, .answer-column-4, .answer-column-5, .answer-column-6, .answer-column-7', q1).click(function () {
        handleHiddenInput (this, 'unchecked');
      });
 
      // A function to toggle the hidden checkboxes 
      function handleHiddenInput(trigger, state) {
        // Identify some stuff
        var rowID = $(trigger).closest('tr.answers-list').attr('id');
        var tmp = rowID.split('X'+q1ID);
        var answerCode = tmp[1];
        var hiddenInput = $('#answer'+sID+'X'+gID+'X'+qHiddenID+answerCode); 
 
        // Toggle the input depending on "state"
        var checkedState = false;
        if(state == 'checked') {
          checkedState = true;
        }
        $(hiddenInput).prop('checked', checkedState);
 
        // Fire the conditions function to hide the corresponding row in Q2
        var hiddenInputValue = $(hiddenInput).attr('value');
        var hiddenInputName = $(hiddenInput).attr('name');
        var hiddenInputType = $(hiddenInput).attr('type');
        checkconditions(hiddenInputValue, hiddenInputName, hiddenInputType);
 
        // Fix up the q2 row background colours
        $('.answers-list:visible', q2).each(function(i, el){
          $(el).removeClass('array1, array2');
          if(i % 2 == 0) {
            $(el).addClass('array2');
          }
          else {
            $(el).addClass('array1');
          }
        });
      }
    }
 
  });
</script>

<script type="text/javascript" charset="utf-8">
   $('#question{QID}').hide();
</script>

{if(Q1_1.NAOK=='A1' OR Q1_1.NAOK=='A2',1,'')}