How to access icloud storage and control sync

I recently added the 20GB storage from the free 5GB. Almost immediate after adding the 20GB storage, I started losing my apps/files from ibooks. I mostly use this unit for our ministry with the Jehovah's Witnesses. I have noticed that after downloading the lost files back to ibook, they seem to be the same files that were there before this disaperance act started taking place. I thank you for any and all help offered!