TL:DR ‘supervisor repair’ worked for me just now
I had recently updated to Home Assistant OS 9.0 (Supervisor 08.6 and Core 2022.9.4)
For some reason my energy meter integration wasn’t working correctly afterwards. Given it connects via USB, I thought I’d reboot the VM (running on a Synology NAS). I watched it reboot and got the ‘system is not ready with state: setup’ error.
I was able to start core manually (core start), but the supervisor remained in a broken state.
‘supervisor reload’ returned ok, but running ‘supervisor info’ returned the same error.
So I tried ‘supervisor repair’, which took a while (and while it was doing so, I found this post), but it fixed everything, including my broken energy meter integration.