I'm really confident that as long as you applied before November 16th, then your application is definitely fine. They wouldn't do otherwise because that would severely affect the whole recruitment process which they can't afford to stuff up right now!
I guess Virgin Australia is pretty much a new airline now, huge changes at every angle. It would make sense to create a brand new website too, to go with the massive influx of new people there is going to be! Thanks heaps to all who have enquired, we have more than enough reassurance now