I don't know if this will help you or not, but I'm having the same problem on an iMac with Yosemite. One thing that I notice is that when I plug my iPad mini in, a copy of the mainDb.sqlite file is created in one of the /var directories. This file is removed when I remove the iPad. When I open this file with an sqlite browser, the file is a valid sqlite file, but it's incomplete, i.e. it only has a couple of books in the books table rather than the 2000+ that it ought to have. If you start calibre in debug mode, you can look through the log and it will tell you where the temporary copy of the mainDb.sqlite file is stored.
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