
I think that message IS complaining about a malformed EPUB and not the OPF found in the books folder.
When you Save To.. or Send... , Calibre updates the internal file of the COPY.
I
was going to say 'You might run the Quality Check (optional) PI ' but I don't see a
specific test for a malformed OPF , but I see that is not a choice

(it may still Barf on other OPF checks, which may be enough info

)