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Since you are using the same dataPoints array on both the chart’s dataSeries and navigator’s dataSeries, any changes made to this array will be reflected on both the dataSeries. In order to remove the indexLabel from the navigator, you can clone an array of the dataPoints for the navigator’s dataSeries using jquery.extend() as shown in the code-snippet below,

navigator: {
    height: 50,
      dataPoints: cloneDPS(dps),

function cloneDPS(dps) {
	var tempDPS = [];
	for(var i = 0; i < dps.length; i++) {
  	tempDPS.push($.extend(true, {}, dps[i]));
  return tempDPS;

Kindly take a look at this updated JSFiddle for an example on the same.

stockChart with indexLabels

Adithya Menon
Team CanvasJS