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I have the same problem with an iPad Air and an iPad mini connecting to an iMac running Yosemite. My current workaround is simply to copy the ebook on to the iPad and iPad mini via the OPDS connection. It's not very satisfactory since the collections info and reading list don't come across that way, so I have to manually set that info on the iPad and iPad mini.
There doesn't seem to be any movement on resolving the issue, at least on the Mac side of things. It doesn't appear that the database is actually corrupt, just that for some reason the iOS plugin can't read the database. It's somewhat frustrating simply because it use to work, now it doesn't and I don't know the person who originally wrote the plugin has dropped the project or not.
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