I haven't tried migrating like that, but there is a foolproof way to find where Reader is opening its books from.
Open the Reader app. Open a book.
Open the Activity Monitor app. Find "Reader for Mac" in the list, select it and click the "i" icon in the toolbar for Info.
Switch to the "Open Files and Ports" tab in Activity Monitor.
One of those lines will be your open book! It'll probably be near the bottom of the list.
Hope that helps :-)
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