[Chartjs]-Chart JS chart not rendering in ArcGIS popup when using navigation arrows

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I think you should not use the text content type for the popuptemplate. Using a function that return HTML element would be easier in your case.

    popupTemplate: {
        title: "{Location}",
        content: createPopup
    }

here your construct your popupElement and insert chart in it:

function createPopup(graphic) {
    try {
        var location = graphic.getAttribute("Location");
        var popupElement = document.createElement("div");
        popupElement.innerHTML = "Sample Location: " + graphic.getAttribute("Type") + "</br> Survey: " + graphic.getAttribute("Survey") + "</br>" + getSurveyInfo(location) + "<div class='chartDiv'></div>"
        var date = new Date();
        var sub = location.substring(0, 2);
        var canvas = document.createElement('canvas');
        var ctx = canvas.getContext('2d');

        getData(date.getFullYear(), [[location]], function(data) {
            var maxScale = Math.max(...data[0].tData);
            var colors = [["#34eb58", "#0000ff"]];
            var chartData = buildChartData(name, maxScale, data, colors, null);
            var chart = new Chart(ctx, chartData);
         }, getChartDataError);

         popupElement.querySelector(".chartDiv").appendChild(canvas);
         return popupElement;
    } catch(error) {
        console.error(error)
    }
}

See working demo: http://jsfiddle.net/bspa906m/3/

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