When I plug my iPhone in to sync I have a "Books" section in the menu of items on my device. In there are some old books that are no longer on my phone, at least that I can see. If I remember correctly, these are just PDFs I originally added, before the days of using iBooks to manage your books. When I click it I see the "Sync Books" section. Ticking the checkbox allows me to select these books but I have no idea why they're still on here -- as I mentioned, I thought these had been deleted long ago.
Even when I choose to sync all books or select particular ones, I don't see any appear on my phone. I am presuming I'd see these in iBooks.
What I do see in iBooks is all the books I have synced using the iBooks macOS app. I see these on all my devices with no issue.
Another, probably related, weirdness is that when I add new items to my library, it inherits some meta data from one of these books in question. For instance I added a PDF in iTunes, and it came up like this in recently added:
This doesn't happen when syncing through iBooks. It looks to be wholly an iTunes issue.
I don't particularly care why it's doing this, although it would be interesting to understand it. Mainly, I'd like to know how do I remove all references to these old books in iTunes so they're no longer in my library?
For completeness, this is what I see when selecting the
File > Move Books from iTunes... in iBooks:
I am using a recent version of iTunes (18.104.22.168) on macOS High Sierra, though this issue has been present for a while after upgrading the OS and transferring my iTunes profile to a new MacBook.
I can provide any more information at request.
When plugging in an iPad I see the following:
This is what I see when searching my iTunes profile for PDFs or EPUBs: