Fixing iBooks on my old Lion-based iTunes server

I have an old 2008 white macbook that is my household iTunes server.  I carefully back it up, but it was not always my iTunes server, and it does not know where iBooks are.  The iTunes library was on a newer machine I upgraded to Mavericks, which moved the iBooks.  I need to fix that before getting an iPhone 6.  I have books not bought from Apple, and PDFs, and I want to keep them on my iPad and iPhone.

I am not using iPhoto on this old machine.  So I have a hole in how I keep backups of photos.  I'll have to look at that later.  It is highly recommended that anyone upgrading iOS make sure that they have a full backup of photos.

I do not have room for my media (photos, iBooks, iTunes) on the local drive, and so have it on an external drive.  I moved the drive from one machine to another, and never migrated iBooks.  Now I have to look for them and update anything that needs updating so that I can again sync iBooks.  Note that audiobooks are still in iTunes - no problems there.  But once iBooks became an app for Macs, iBooks were no longer in iTunes.

I have my iBooks on my Mavericks-based machine.  Where?

• ~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/Books

So I copied files from my Mavericks computer to a location available to my iTunes server computer.  I tried to import them.  It turns out I had some of the files located on my old Lion-based iTunes machine, so I deleted duplicates.  I tried to sync my iPhone.  It said it could not locate some files.  I ended up deleting ALL iBooks from my iTunes library, unselected all books from sharing with my iPhone, and then reimported the whole list in the shared location.  I still had no PDFs; importing PDFs did not work.  I had to drag and drop the PDFs into iTunes in my old iTunes server.   I then selected books (and PDFs) to sync, and it all worked.  Whew.

The good thing is that I had put some PDFs into categories in iBooks on my iPhone and iPad.  They fell right back into those categories once re-synced even after all of my cleanup shenanigans.  I did not have to re-select the 15 PDFs related to a class I took into a category for that class.