How can I redirect iTunes to my ebooks after it lost track of them, so I can get back in sync without erasing the books (and notes) on my iPad?

What I need is for my books which are on my iPad to be synced to my mac, and not vice versa.
The iTunes library lost track of all of my media. Everything's still there and for songs its no big deal to simply reimport (from the directory which never moved, but which iTunes stopped pointing to for some reason.) But for my books, which have notes and highlights, I don't want to erase whats on my iPad and resync with the current state of my books on my mac

I will address your second question.
First, make sure your iPhone and iPad have absolutely identical Apple IDs.  If they do, use that Apple ID in Settings > iCloud on your iPhone to select the "Notes" option.  Lo and behold, all your iCloud notes should appear on your iPhone.

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