Ibooks on mac does not sync with ibooks ios

i have about 50 books, not all bought, showing in my ibooks on mac. However on my iphone i have only about six. I have followed the instrucitons to check Show All Purchases but as the items were not all purchased via ibooks i am wondering if iOS ibooks only shows items purchased via the store..
Thanks for any ideas

I found a solution that worked for me.
I had books that were not purchased from iTunes and some that were  in my iPhone iBooks and they were not in iBooks on my macbookair.
I went into itunes -  then File / Devices  - select Transfer purchases from iPhone.
voila after restarting iBooks  they appeared on my Macbookair.
hope that helps others.

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