I recently had an interesting experience adding an ePub to my Books application on my Mac desktop. This came about because I find it a bit easier to select a story and read it using the Books app.
The situation occurred after adding several ePubs to the Book library app with no issues. In some case these were dates of already loaded ePubs. And then one ePub would not load into books. Several attempts were made and some were with a freshly download copy. At first I thought it was a file corruption issue but our admin checked and found it loaded fine on his iPad. So...while I could just let it be, things that don't work when they should bother me.
After futzing around trying various solution paths, I found one that worked. Like our admin, the book loaded fine on to my iPad. So I exported it from the iPad to a file on the Mac. The exported file loaded in to Book Library with no issues. As to exporting the ePub from the iPad, I used an iTune alternative, which also provides some other tools to use.
So if you are having troubles loading a ePub, you might want to take the in direct approach.
Hope this information is valuable to someone.
Cheers