I had accidentally reinstalled the Navigraph data to the RJ a couple weeks ago, and I forgot to go double check. So just now I loaded in at YPPH Perth, which is where I first noted the issue, and ascertained that neither YPPH nor YSSY are in the database. It's a shame, because the RJ is the only fully-functional, non-bug-infested airliner I have in the sim, so I'd love to have all the navigation data loaded into it!
Edit: Thankfully, the 2020 version of the RJ doesn't have this navdata problem, so I can do all the Australia flying I want in that sim.