I'm using iBooks Author to write the embedXcode User Manual. I'm exporting the User Manual directly to the iBookstore, and I'm also generating a PDF.
Unfortunately, Preview can't display such a PDF. This is due to a bug, for which I filled a ticket with Apple.
I opened a ticket #100165721037 last May 18, 2017. Despite two macOS updates, and after multiple and lengthy contacts with Apple Support, the ticket is still unsolved.
So please contact Apple Support ⓦ directly.