Apple Books corrupted my book and wiped all my PDF highlights

I am using Apple Books on my iPad and I noticed a very frustrating issue. Books that I download for offline reading are continuously being deleted by the app. It seems that the system keeps uploading to iCloud and then removing the local files, even though I want to keep them on my device.

As a result, one of my books became corrupted and I cannot open it anymore. Even worse, all the notes and highlights I made inside a PDF book were also lost when this happened. This makes Apple Books unreliable for study or work, since important annotations can suddenly disappear.

I have already tried disabling and re-enabling iCloud Drive, and re-downloading the books, but the problem still happens. So, how can I :

1. Upload books to iCloud for backup/sync,
2. But never automatically delete the offline copy or user notes unless I choose to.