I am having the same problem with my iphone 6S plus (iOS 9) that I just purchased. I was going to upgrade from the original ipad mini and wish I had checked the forums first. I use Calibre to organize my extensive ebook collection and used it to sync with Marvin so I could read on my ipad mini.
Is there another ebook reader out there for ios that will communicate with calibre in order to send/organize a large number of ebooks? It's ironic, the reason I switched from a Kindle was due to the lack of organization for collections and I found Marvin and was very satisfied until it stopped communicating.
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