IBooks grabbed books from Dropbox

I installed Mavericks last night.
When I opened iBooks on my desktop, iBooks went out and moved files from my iTunes books library and moved them into the iBooks library.  As intended by the program, I guess.
However, my iTunes book library was referenced to my Dropbox, where I keep all my ebooks, mostly in .epub form.
I think the problem is that, unlike iTunes, where you can disable copying files into iTunes library, iBooks doesn't allow for this.  No setting in Preferences, anyway.
So, now the books are gone from Dropbox...where I could access them from my iPhone or iPad or whatever.  And they are renamed in the cryptic iTunes mumbo jumbo file type.  The real name of the book doesn't show up in Get Info.  So that piece of metadata isn't easily accessible.  In the iBooks library file list the book is there by title...but you can't move it, etc.
VERY frustrating.  Short of opening each book, finding out the title, renaming and physically moving it back to the Dropbox, and then getting rid of iBooks, I seem to be out of luck for a fix.
The files in the library can't be accessed from iOS...unless purchased from Apple.  And we are talking about 1.4 Gb of files.
I am NOT pleased.  Have sent feedback to Apple...but this isn't going to fix squat. 
Unless someone else has an idea.
Regards

Hi
I just received my iPad2 yesterday. The books that I purchased through iBook on my iPod appear in my iTunes Library. They also appear in the synchronisation window for my iPad. When I synchronised my iPad for the first time, the movies I had selected to add to my iPad did not synchronise but all of my books synchronised. When I synchronised my iPad again, the movies eventually added, but I didn't notice until today that all of my books disappeared. I have tried several times to synchronise my books today, but to no avail. I tried to sync all books and then I tried to sync selected books but nothing worked. I have located the book files and they are all in my iTunes folders. Does anyone have any advice? Has anyone else had this problem?

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