That is not an 'error' (at least to Calibre

)
What you see is a very legitimate usage called an empty book.
There are 419 in my Library. These document books that exist in Dead Tree (Format)

in the storeroom.
Another common usage:
Wishlist of things to come
Library Maintenance verified the Library matched what was found.
(The Library is really The DATABASE of what you have added / changed )
Since there were no integrity errors, that said one of two things: 1)You use Calibre properly (not by going under the skirts in the OS) to remove the format. 2) You had created an
empty book entry.
The only unknown: Intent. Were either of those what you really wanted to do?

We can't answer that one.