I believe the visual studio command for this is "Project.UpdateServiceReference". So I guess you can try to select the node you're interested in, and run this command, like this:

envDTE.Windows.Item(vsWindowKindSolutionExplorer).Activate();
envDTE.ActiveWindow.Object.GetItem(@"MyProject\Service References\Proxy").Select(vsUISelectionType.vsUISelectionTypeSelect);
envDTE.ExecuteCommand("Project.UpdateServiceReference");