I have no idea what happened here.
From CC's point of view the books (news articles?) existed. It asked calibre for metadata and received something that looked like metadata. It asked calibre for the book file and received something legitimate. I don't log the file length so I don't know whether what it received actually had content or was zero-length.
There is nothing unusual in the debug logs.
Unfortunately calibre debug logs do not contain the content server logs so I can't see what it thought, but I suspect it thought everything was fine. It would report an error if the files weren't there. It doesn't care if the files are zero length.
What it looks like is that the file system under the content server reported files as existing but gave a zero-length file when a file was opened. That would account for the missing cover and the missing content. All the rest comes out of metadata.db, which is read into memory when the content server starts. Any file system hickup after that wouldn't affect providing metadata. Why a file system would behave in this way is a mystery. Is there some kind of sync program involved? Could something have locked the files, perhaps a sync or backup program?