Some pdf's that show up in my ibooks on my mac do not show up when I try to sync through itunes. Can't figure out why.

The transfer from my itunes book library to ibooks app on my mac (mavericks) went fine. The problems started when I tried syncing. The first time, everything went fine. Pdf's and ebooks showed up on my devices. I then added more pdf's to ibooks on my mac and when I tried to sync them with my devices, some show up and some don't. I thought it might have something to do with file size but again, some large pdf files did show up in tunes and some didn't.
Overall, not all things are mirroring like they are supposed to between the ibooks app on my mac and itunes, resulting in not being able to get all the content I want on to my devices via syncing.
For example, I will delete something out of ibooks but it stays in itunes when I go to sync. I'll delete it from all the devices and the computer and it will still be in itunes and will reload onto my ipad when I sync my entire library. To repeat, I deleted a book out of ibooks but it still shows up in itunes when I go to sync. Other books that I delete from ibooks do disapear from itunes and are no longer availalble for syncing, as it should be.
There was a pdf I changed to an epub in Calibre. I converted it in case the large size of the pdf was a problem. As an epub, it was a smaller file (8.6 mb vs 100 mb). I deleted the pdf from all devices and the ibooks app. I reloaded it into ibooks as an ebook. It showed up fine. I was able to open it with no problems. Went to sync it with itunes and it didn't show up nor appear on my ipad after syncing the entire library.
So, ibooks on computer is working fine. The content is there (or not there when I delete it) in what ever format I want it. I can open and read everything just fine. The problem is trying to get that same content onto my devices via itunes. Why does some content transfet just fine and some doesn't? Why does some content delete fine while other content can't be deleted from itunes? Why do some pdf's load fine in itunes and some won't?
My computer and my devices all have current updates.
Help!

I had the same issue. After searching around online I found out that you can try downloading another app (it can be any app) onto your ipod. After it finishes downloading see if your other apps open. You don't even have to keep the new app. Just see if your other ones work and you can delete the new one. That should work. If not, try to hard reset it. Here is another apple support link for steps on hard reseting it (http://support.apple.com/kb/HT1430).

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