Android - open or restart app after clicking push notification using flag activities

You need to set the Intent flags on the Intent. You were specifying them in the call to get a PendingIntent. Try this:

notificationIntent.addFlags(Intent.FLAG_ACTIVITY_CLEAR_TOP | 
    Intent.FLAG_ACTIVITY_SINGLE_TOP | 
    Intent.FLAG_ACTIVITY_NEW_TASK);
PendingIntent contentIntent = PendingIntent.getActivity(this, 0,
    notificationIntent, 0);