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Yes, the new iTunes was a pretty big change. It broke some of the tools that I use to format shift my various digital purchases as well. Hopefully the various tool vendors will update to fix the issue. The vendor I use to format shift my video already has a fix in. Hopefully, the audiobook tool fix from the same vendor will come out soon.
The issue with copying from calibre companion to iBook/Marvin/whatever is a change in how ios interacts between programs. That will require a update for calibre companion. Download via the safari web browser and opening in iBooks works.
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