I have been debating as to whether or not to post this problem for a few days. I finally decided that it may help someone in the future.
I have one book that I downloaded from AO3, using FanFicFare, as an Anthology:
Harriet Potter and the marvel universe Omnibus by Maddalice13.
On sending it to my KOBO Clara HD eReader it came back as present on device. However, on ejecting the device there were no progress bars and the book was not in MyBooks. Searching the KOBO filesystem showed that the EPUB file was in the correct place, so it had to be a database problem.
Having read several threads on this board that indicted that it could by an EPUB formatting problem, I used the calibre editor to check and clean up the EPUB. Still not loading.
After trying a number of different thing, I started to think outside the box and changed the author from "Maddalice13· to "Madd alice"; which actually worked.
This has really confused me as I read a lot of fan fiction and I have a lot for books with author names that fit the pattern "^[A-Za-z]+[0-9]+$". As a final test I sent a different book with an author name matching the pattern "^[A-Z][a-z]+13$", which worked.