There is a problem with iBooks: books are getting removed locally and uploaded to the cloud, if the space is running low on the device. But with iOS 11 some users experience unwanted file upload even when there is no space shortage.
But actually there two ways to solve the issue:
- Remove iBooks
Reinstall it from AppStore
Download all the books.
It might be useful also to do this afterwards:Settings > Apple ID > iCloud > iBooks: OFF
Settings > Apple ID > iCloud > iBooks: ON
- Check the appropriate settings, stop iCloud syncing at:
Settings > iBooks >Sync Collection: OFF
Settings > Apple ID > iCloud > iBooks: OFF
And then upload books to the device using wire, or just get them through Cloud Storage (Dropbox, Google Drive, Yandex.Disk or etc).