What you describe is an 'Empty Book' (metadata only). IMHO useful to keep track of books belonging to a series, but not owned. Public Library books that have been read (and the book checked back in
)
This is a 100% valid condition, which is why the maintenance did not flag it.
If someone HAD gone into the file system and deleted the format, the error would be flagged (Calibre keeps track of formats stored) as MISSING.