I don't have an actual solution (I'll leave that to the more technical minds on the forum), but a brief workaround until it gets sorted is that the new iBooks application allows you to add books (File-->Add to Library). I did this yesterday and added a book I wanted from where it were stored on my computer in my calibre library.
Obviously not a long-term solution, particularly with a big library (since you have to go inside each ebook file to find the .epub file), but it's a short-term option if you're just looking to get a book onto your ipad/iphone/ipod/etc. so that you can read it until a real solution is figured out.
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