Even if you attempt not to quit iTunes, you eventually may have to (as I did during a recent power outage), causing all the epubs to be reclassified as audiobooks again. Rather than face the prospect of calling up Get Info individually for each book to force it to revert to an ebook, there is a way to process them all at once.
1. When viewing the Audiobook list (including the wrongly classified epubs), go to the View Menu and Show the Column Browser. Be sure that 'Kinds' is checkmarked.
2. In the Column Browser, click on Books. This should cause all the incorrectly classified ebooks to be listed, and nothing else.
3. Select All, then Get Info.
4. Within the Get Info window, change the Genre to something (Books, Fiction, Writing, etc.). It doesn't matter what you choose; it will not affect the Category of the book within iBooks after each file is recognized as an epub.
5. Click OK. All the highlighted books in the list now will rapidly be converted back to epubs, so they can be synced with your ipad or other ios device.
This still isn't a permanent fix. (FIX THIS APPLE.) But it makes temporary fixes after a restart of iTunes much more efficient.
Hope this helps.