IBooks Mac not working

Ever since I consolidated my files in iTunes my iBooks library has not be working. All existing downloaded books can not be opened or deleted. Anyone experiencing the same problem? Any help would be appreciated!

Yes, I am experiencing similar problems.  I understand the thinking here (I think).  iBooks is the book depository where you can manipulate your library and iTunes is just for audio and for syncing.  I transferred my books and PDFs to iBooks 1.0.1 (as instructed) and iBooks seems to work fine for me on my MacBook Pro (Mavericks 10.9.1).  However, iTunes seems to have retained the old database of books and when I update the Mac iBooks library,  iTunes does not seem to know about the Mac iBooks database. When I sync, it just uses the old library that iTunes knew about before the Mavericks update, and it doesn't handle any updates.  I tried the option key while opening iTunes to select a new library, but the iBooks library is not visible there.  Effectively, I cannot sync the Mac iBooks to my iPad iBooks. 
I am a reserch mathematician, so I download PDF journal articles to read on my ipad.  The turnover is pretty fast.  This is not the sort of information you can find in a book or eBook. Without being able to sync, iBooks on the iPad becomes useless for me.  Some people have suggested a work around by using eMail, but that doesn't send the metadata, and some of the articles are larger than the 25 meg limit on my eMailer. 
Do we just have to wait for the next version of Mac iBooks and iTunes so they can talk to each other ?

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