Well, the problem has gone, but I'm not sure why.
I have run check disk before without success, but I ran it again just in case and I still got the error message at first. I didn't do anything else, but after one more failed restart the problem disappeared.
Does this make any sense? Could check disk have had a delayed effect or has the problem spontaneously fixed itself?
I'll work through the Microsoft article if the problem returns. I notice in the article though that it says the problem occurs during startup, as do all the other instances of this error message that I have come across online. I can't seem to find any examples where the message appears while shutting down.
Thanks for the help, with any luck I won't need more on this problem.