Apple iBooks generally does a good job of managing your collections of books and PDF. But, you know, sometimes shit happens and your contents are gone. This happened to me a few days ago. Where should you look in your filesystem and in your backups to restore your books and your PDFs?
First of all, don’t worry for the books you bought on the iBooks Store: they can be re-downloaded from the store at any time. You can even choose not to have a local copy and to fetch them on demand.
The real problem here are the PDFs that you manually loaded on iBooks and can be synchronized with iCloud.
So, where are the files stored?
The e-books you bought on the iBooks Store and all the local contents (those books not in iCloud) are stored in:
Instead, the books that are in iCloud and are synced with all your devices are in:
(that’s an hidden folder, you can reach that using the Terminal).
This information is useful if you have a backup and can restore the files in these folders. This will not restore your collections, but at least you will have your files back.
I haven’t still found a reliable way to backup or restore the entire iBooks database (books and collections) if iCloud fails. This problem is open for further research. 🙂
Check iCloud settings
Another thing worth mentioning is to check whether iCloud is syncing or not your books. This settings is hidden in the iCloud preferences in macOS, and can cause some headaches, specifically partial or incorrect synchronization.
Also, there is an option in the preferences of the iBooks app to synchronize your collections. Make sure it’s enabled if you want to sync: