Books automatically deletes my books when offline, and when there is enough space on device
I feel you. I've never been able to figure this out, and it is so frustrating. This might not be the answer you're looking for, however, I've migrated away from using iBooks and using iCloud for syncing anything besides things like the keychain and settings.

Since you mentioned you were reading a pdf ebook, I recommend an app called Bluefire Reader. It does ePub, PDF, and Adobe DRM. Of course, if you have a bunch of ebooks you've bought from Apple, well, that's another thing; DeDRM does exist, but that's really all I can say on that.