Hmm. I never delete my books on the pc just in case the devices lose them. If they were on iBooks, they would be automatically saved on the iCloud as that is how I have set it up on my devices using the manage backup in settings-iCloud. I'm afraid you will have to wait for TwerpPoet who is a lot cleverer than me when it comes to ebooks. Sorry! Keep trying though. A lot of my problems I've solved on my own just by surfing the net.
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