Here's my html:

<div class="timer">Not Started</div>

And JS/JQ:

var seconds = 10;
  var minutes = 0;

  setTimeout("updateTimer()", 1000);

  function updateTimer() {

     if (seconds == 0 && minutes != 0) {
        minutes -= minutes;
        seconds = 59;
        alert (seconds);
     } else if (seconds == 1 && minutes == 0) {
        alert ('done');
     } else {
        seconds = seconds - 1;
        //alert (seconds);
        $(".timer").replaceWith(seconds);

     }

     setTimeout("updateTimer()", 1000);

  }

Instead of replacing Not Started with 10, 9, 8..., Not Started disappears.