When the selected item is removed, new current and selected Appointment is set. When new selection is performed, Scheduleview focuses the selected container and MsToolTip opens when the container with tooltip receives keyboard focus. 
Workaround for tis behavior is to suspend notifications when removing selected apps one by one:

         RadObservableCollection<Appointment> apps = new RadObservableCollection<Appointment>();
....

            updateTimer.Tick += (s, e) =>
            {
                Application.Current.Dispatcher.Invoke(() =>
                {
                    apps.SuspendNotifications();
                    apps.Remove(appo1);
                    apps.Remove(appo2);
                    apps.Remove(appo3);

                    apps.Add(appo1);
                    apps.Add(appo2);
                    apps.Add(appo3);
                    apps.ResumeNotifications();
                });