Originally Posted by Manichean
The root folder should only contain metadata.db, so the file is at least out of place. Did you do some manual copying inside the library? What does the metadata inside the metadata.opf look like (open in text editor)?
I too have a metadata.opf in the root of my library. The last time I just deleted it but your question intrigued me so I checked it out prior to deleting it. It turns out it was the last book I added to my library. I'm not sure why calibre stashed it there. Maybe I'll be able to develop a trend as I find these files.