Ibooks, ipad, itunes, ios 8 problem

i, like most people, have their ebooks from various sources, B&N, ibook store, friends, etc.... Here is the problem i am fighting. I will load a number of books on my iPad some from ibooks, some from B&N etc. All the books will load on the ipad and are checked in iTunes. the status bar shows the books are there, if i look at what is on the device the books are there, all is working well.
If i connect the ipad a couple days later here is what happens....
itunes has no books checked
on my device shows only the 5 books that i have purchased from ibooks store
all of the books are still on the ipad, but if i want to add another synching will erase all the books currently on the ipad and only sync the one i chose and the ones from the ibooks store.
this problem began with ios 8. i have been in conversations with apple and have a case opened with the engineering people. i was hoping 8.1.3 would help it did not. Has anyone else had this problem? thanks in advance for the assistance
rjherald

Same issue here, iBooks on MBP retina shows list checked. At random instances of syncing, my iPad will lose every book, PDFs etc, except those purchased through Apple. I cannot duplicate issue, so I don't know why sometimes sync works fine and next time, entire contents of iBooks vanishes save Apple Store purchases. I also cannot find a way to permanently delete those books and/or pdf's I no longer want from iTunes "books" screen, so when syncing deletes files, trying to recreate what I want is pretty tedious, since I have to go through a list
of every book and pdf ever present on MBPr.
ANyone know now how to prevent the loss of books during sync fromIOS device?

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Ibooks, ipad, itunes, ios 8 problem

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