[Network] Fixes for loading of examples (#3332)

This PR contains two small fixes to ensure that all examples rung.
I noticed that some examples weren't working, so I tested them all.

lib/network/Network.js

@@ -273,6 +273,9 @@ Network.prototype._updateVisibleIndices = function () {
 
       if (!this.clustering._isClusteredEdge(edgeId)
         && edge.options.hidden === false
+        // Not all nodes may be present due to interim refresh
+        && nodes[edge.fromId] !== undefined
+        && nodes[edge.toId  ] !== undefined 
         // Also hidden if any of its connecting nodes are hidden
         && nodes[edge.fromId].options.hidden === false
         && nodes[edge.toId  ].options.hidden === false) {

lib/network/modules/PhysicsEngine.js

@@ -134,6 +134,11 @@ class PhysicsEngine {
         this.physicsEnabled = false;
         this.stopSimulation();
       }
+      else if (options === true) {
+        this.options.enabled = true;
+        this.physicsEnabled = true;
+        this.startSimulation();
+      }
       else {
         this.physicsEnabled = true;
         util.selectiveNotDeepExtend(['stabilization'], this.options, options);