From other discussions I have discovered that I am not alone in not being able to sync pdf's from my iPad to other devices. As well as pdfs not synching, I have just discovered that purchased books won't sync if Apple has dropped the titles. I recently bought a new iPhone and noticed that it had synced from my iPad all my purchased books less one and none of my pdfs. When I checked out the missing purchased book I discovered that it had been removed from the store. Therefore, purchased books, like apps, are not available from the cloud and so can't be synced if they are no longer current.