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@satyabratacanvas,
The issue is happening as minimum and maximum are being updated on hiding and unhiding the dataSeries. I would suggest you to update viewportMinimum and viewportMaximum instead. Please find the code-snippet below.
chart.options.axisY.viewportMinimum = chart.axisY[0].viewportMinimum; chart.options.axisY.viewportMaximum = chart.axisY[0].viewportMaximum; chart.options.axisY.interval = chart.axisY[0].interval; chart.options.axisY2.viewportMinimum = chart.axisY2[0].viewportMinimum; chart.options.axisY2.viewportMaximum = chart.axisY2[0].viewportMaximum; chart.options.axisY2.interval = chart.axisY2[0].interval;
Please take a look at this updated JSFiddle for complete code.
— Vishwas R Team CanvasJS