This is very bad. After exiting and restarting EiffelStudio, I hit F7 again. The same internal error occurred.

This time I clicked the Restart button. When the start-up dialog appeared, I selected Freeze from the combo box. Again the same error occurred.

I clicked the Restart button again. This time in the start-up dialog I selected Freeze and Clean. A "Configuration Loading Error" dialog appeared: "Cannot create project in ... You may try again after fixing the permissions." I didn't have that directory open as far as I was aware, so I checked Process Explorer. It found TortoiseProc, and then I realised what the cause was: just before the first failed compilation, I had run an external command:

start tortoiseproc /command:log /path:"$file_name" /notempfile

This was still running, and it had the project's directory open for some reason. I closed the Tortoise Log window and then tried Freeze and Clean again. This time it succeeded.