You know for a fact that you have a specific PDF pattern saved in your iBooks….and suddenly you are missing some files! If that happened to you after an IOS update, no need to panic, these files can be easily recovered from iCloud in 3 simple steps. If you have multiple Apple devices connected to the same ID (example – iPhone & iPad), I would recommend to go through these steps on all devices at the same time.
Close iBooks app & go to Settings > Apple ID > iCloud
Scroll down to find iBooks icon and switch the green slider to the OFF position.
Wait about 20+ seconds….NO rush or it won’t work! Now reset your device. For example, if you have an iPad —> press & hold the Home button + Power button at the same time until you see the Apple logo.
Once your device is reset & ready to use, go again to Settings > Apple ID > iCloud & turn the slider for iBooks back to ON position (it should be green).
Now open your app and the missing files should be restored from iCloud. If you still do not see missing files, tap on “Collections” at the very top of the screen and make sure that you see “All Books” & the “Hide iCloud Books” is in the OFF position.
This article is based on my personal experience; please understand that I do not have answers for different app-related issues. There might be different reasons for similar issues and different ways to fix them. I am not a certified specialist, you can contact Apple support if you need additional help with Apple product.