I have the same issue: Unable to manage iBooks in iTunes
With the new iTunes version 12.7 and IOS 11.0.1, iBooks can no longer be managed from iTunes. I have about 200 important documents, pdfs, on my iPad and iPhone. In all previous versions of iTunes, these documents were accessible and manageable in iTunes, and it was possible to place them in categories, document the authors, adjust the titles, etc., and then to sync all my devices to insure the documents were consistently available on either of my apple devices or my Windows 10 computer.
With the new Files app, I am able to add documents to my devices and even read them in iBooks, but they are not stored in iBooks and cannot be sorted or placed into categories with other related documents. Many of the documents already in iBooks are updated periodically, but with the new operating systems, all I can do is delete the older versions in iBooks and place the new version in the iCloud Drive which is now in the Files app. The old iCloud Drive app at least allowed these documents to be imported to iBooks, but I'd have to do that on both my iPhone and iPad.
I've left detailed feedback with Apple, but no response and no sympathy. Am I the only one troubled by this loss of functionality? This change rendered iBooks essentially useless.