Downloaded ibooks get deleted when icloud sync is turned off, even under airplane mode Recently, I had all my iBooks deleted from local storage as detailed in this question: Books automatically deletes my books when offline, and when there is enough space on device. 
I went through and downloaded all the books to local storage by tapping them. I believe that they are in local storage as they can be read on airplane mode, but they do not appear in iphone storage. However, turning off icloud sync of ibooks: settings -> Apple ID, iCloud... -> iCloud -> Books causes all the books to be deleted or hidden from my iphone, even if the phone is on airplane mode. How would I go about recovering these books without leaving sync on as it would delete the books again?
You need to get those books on iPhone via methods other than iCloud sync to keep them there with sync off.

Use airdrop to get the books onto iPhone, open them with Books app and then you can turn off sync and books won't get deleted. That's how, I understand, it works.