Hi there, I just wanted to reply to mention I have the same issue.
IFR seems completely broken, this started for me with SU9. I’m on XBox.
I created a post a few days ago about this: https://forums.flightsimulator.com/t/ils-not-working-correctly-since-su9-xbox/
To summarize though, airports I’ve been flying IFR with using ILS since release I can’t setup either for anymore. All the NAV IFR waypoints seem missing, and ILS doesn’t work. In fact, I used to be able to select an ILS runway in the drop down for the airports prior, now the only option I get is “automatic”.
Very frustrating. I was hoping the patch they just released would fix the problems but I just tested and they are still there.