removed nodes and edges from the selection before they are deleted through the dataset or when setData is called.

lib/network/Network.js

@@ -603,6 +603,10 @@ Network.prototype.setData = function(data, disableStart) {
   if (disableStart === undefined) {
     disableStart = false;
   }
+
+  // unselect all to ensure no selections from old data are carried over.
+  this._unselectAll(true);
+
   // we set initializing to true to ensure that the hierarchical layout is not performed until both nodes and edges are added.
   this.initializing = true;
 
@@ -1684,10 +1688,22 @@ Network.prototype._markAllEdgesAsDirty = function() {
  */
 Network.prototype._removeNodes = function(ids) {
   var nodes = this.nodes;
+
+  // remove from selection
+  for (var i = 0, len = ids.length; i < len; i++) {
+    if (this.selectionObj.nodes[ids[i]] !== undefined) {
+      this.nodes[ids[i]].unselect();
+      this._removeFromSelection(this.nodes[ids[i]]);
+    }
+  }
+
   for (var i = 0, len = ids.length; i < len; i++) {
     var id = ids[i];
     delete nodes[id];
   }
+
+
+
   this._updateNodeIndexList();
   if (this.constants.hierarchicalLayout.enabled == true && this.initializing == false) {
     this._resetLevels();
@@ -1819,6 +1835,15 @@ Network.prototype._updateEdges = function (ids) {
  */
 Network.prototype._removeEdges = function (ids) {
   var edges = this.edges;
+
+  // remove from selection
+  for (var i = 0, len = ids.length; i < len; i++) {
+    if (this.selectionObj.edges[ids[i]] !== undefined) {
+      edges[ids[i]].unselect();
+      this._removeFromSelection(edges[ids[i]]);
+    }
+  }
+
   for (var i = 0, len = ids.length; i < len; i++) {
     var id = ids[i];
     var edge = edges[id];