iCloud removes my third-party ePubs and PDFs from my iPad without permission — how do I stop this?
It sounds like you have "Automatically Manage Storage" turned on in the preferences. If the device is almost filled up, then iOS could be deleting iBooks that are available from your iCloud account from the device.

You can re-download them from iCloud when needed. Bookmarks, placemarks, etc. are also saved into iCloud.