$("#checkbox1").attr("checked", $("#checkbox2").attr("checked"))

<asp:CheckBox runat="server" ID="CheckBox1" onclick="checkBoxChanged1(this)" />
<asp:CheckBox runat="server" ID="CheckBox2" onclick="checkBoxChanged2(this)"/>

<script type="text/javascript">
var checkBox1 = document.getElementById("<%=CheckBox1.ClientID %>");
var checkBox2 = document.getElementById("<%=CheckBox2.ClientID %>");
function checkBoxChanged1(e)
{
    checkBox2.checked = e.checked;
}
function checkBoxChanged2(e)
{
    checkBox1.checked = e.checked;
}
</script>

<script type="text/javascript">
  $(function(){
       $("#<%=CheckBox1.ClientID %>").click(function(){
    	   $("#<%=CheckBox2.ClientID %>").checked = this.checked;
        });
       $("#<%=CheckBox2.ClientID %>").click(function(){
    	   $("#<%=CheckBox1.ClientID %>").checked = this.checked;
        });
   });
</script>