When update() is called, we need to reset the tooltip.

src/core/core.controller.js

@@ -371,6 +371,14 @@ module.exports = function(Chart) {
 
 			me.updateDatasets();
 
+			// Need to reset tooltip in case it is displayed with elements that are removed
+			// after update.
+			me.tooltip.initialize();
+
+			// Last active contains items that were previously in the tooltip.
+			// When we reset the tooltip, we need to clear it
+			me.lastActive = [];
+
 			// Do this before render so that any plugins that need final scale updates can use it
 			plugins.notify(me, 'afterUpdate');
 

src/core/core.tooltip.js

@@ -384,6 +384,7 @@ module.exports = function(Chart) {
 	Chart.Tooltip = Element.extend({
 		initialize: function() {
 			this._model = getBaseModel(this._options);
+			this._lastActive = [];
 		},
 
 		// Get the title

test/specs/core.controller.tests.js

@@ -822,6 +822,54 @@ describe('Chart', function() {
 			expect(chart.tooltip._options).toEqual(jasmine.objectContaining(newTooltipConfig));
 		});
 
+		it ('should reset the tooltip on update', function() {
+			var chart = acquireChart({
+				type: 'line',
+				data: {
+					labels: ['A', 'B', 'C', 'D'],
+					datasets: [{
+						data: [10, 20, 30, 100]
+					}]
+				},
+				options: {
+					responsive: true,
+					tooltip: {
+						mode: 'nearest'
+					}
+				}
+			});
+
+			// Trigger an event over top of a point to
+			// put an item into the tooltip
+			var meta = chart.getDatasetMeta(0);
+			var point = meta.data[1];
+
+			var node = chart.canvas;
+			var rect = node.getBoundingClientRect();
+
+			var evt = new MouseEvent('mousemove', {
+				view: window,
+				bubbles: true,
+				cancelable: true,
+				clientX: rect.left + point._model.x,
+				clientY: 0
+			});
+
+			// Manually trigger rather than having an async test
+			node.dispatchEvent(evt);
+
+			// Check and see if tooltip was displayed
+			var tooltip = chart.tooltip;
+
+			expect(chart.lastActive).toEqual([point]);
+			expect(tooltip._lastActive).toEqual([]);
+
+			// Update and confirm tooltip is reset
+			chart.update();
+			expect(chart.lastActive).toEqual([]);
+			expect(tooltip._lastActive).toEqual([]);
+		});
+
 		it ('should update the metadata', function() {
 			var cfg = {
 				data: {