Delete the Book from the iPad, then visit the iBooks Store in iBooks, go to the Purchased tab at the bottom, and re-download the book directly to the iPad. This will only work with iBook Store purchases, obviously.
Ooo how frustrating. Many of my books are not from the iBook store so what I did was delete them from my ipad AND then I also deleted them from iTunes, (having kept copies elsewhere of course!). Then I re-loaded them into iTunes and then synched onto the iPad and hey presto...it was a bit of a perfromance mind you!
Ok, That did it, and it worked. It is a bit of a pain, but it works if you care about the cover art. In detail, here is what I did. I went to the folder on my computer where all the books are stored. It is in the home folder (a little house on my Mac). Then, I opened the "Music" file. Inside that, I opened "iTunes Media" and then "books". In that folder are all the books I have ever downloaded, sorted by author. They get put in there automatically by iTunes, I guess, I did not set up the folder.
To be safe (since iTunes put them there, it could probably remove it, as well), I moved the files with the books with no cover art to the desktop. Then, I opened iTunes and deleted the books from the library. I then removed the same books from the iPad library.
Going back to iTunes, I added the books on the desktop to the iTunes library. They came with the cover art I had previously, so I did not have to get it from Google again. Then, I synched my iPad, and the books, with cover art, appeared again in all their glory. By the way, after adding the books, the ones I had removed from the iTunes media file we placed back in there again by iTunes.
Thank you to all who helped out with this rather annoying issue.
Glad you got it fixed. No idea why you had to go to that extent but at least it worked.