Lost my notes and bookmarks in the book app in syncing

Hi,

I read quite some books with the standard Apple book app. I did a backup to my notebook. I noticed that some books were missing on the notebook and tried to sync them. This somehow failed and the bookmarks and notes were not transfered to the notebook. The book that I was reading on the iPad was missing there.

I tried to reinstall the iPad and now most of my books are missing on the iPad and I guess my notes are gone as well, which is a disaster.

Any hints on what to do and how to prevent this in future? Is apple assuming that everybody is using iCloud for this bookmark and book stuff?

I do not.