Not surprising. Have a config backup? If not, make one now and hope it's ok.
In either case, reinstall FreeNAS to new media and upload the config file. Consider using mirrored boot devices to make for an easier recovery from these situations.
Yes, I have a config backup.
So for now I can use the server, as long as I'm not rebooting - is that correct? I want to order 2 good usb drives and mirror them.