I have this problem too.
Anything that I purchased from the iBooks store is syncing fine. But all epubs from any other source no longer show up in iTunes as syncable with my phone when its connected.
One temporary workaround I found, is go into iTunes and on each file listed as an audiobook that should be a book, select Get Info. That will cause iTunes to move the file to its Books tab (not iBooks, mind you, but the iTunes Books tab). You can only do this one at a time, unfortunately (meaning you can't select all the files at once and have it work). Once each book is re-recognized as a book, those books will now show up in iTunes as being syncable with your device. You can then sync and get your books back. It even keeps the organization/categories you had set up before.
It's only a temporary workaround, however, because as soon as you quit iTunes and reopen it for any reason, those files will be moved to iBooks, and all your non-Apple iBooks will again disappear from iTunes, and you'll be and you'll be forced to do the whole thing over again.
I actually called Apple Support on this, and they were baffled. Hopefully a fix comes before IOS 9, which is still probably 6 weeks away or so.
The good news is that the source files themselves are NOT being relabeled as audiobooks in the file extensions, since I can read them just fine in iBooks for Mac. So at least there's that. 😟
