Still ongoing.
I have tested if somehow compression was involved, I downloaded books I had brought previously as uncompressed and added them to Ibooks, They where eventually removed.
I tested if it was something to do with newer books vs older books I downloaded books I brought over the last 10 years. They where eventually removed.
I did observe some curious behaviour today. I added 4 books to Ibooks, I then synced, the status bar said it synced all 4. they where not in iBooks for the iPad, they where in iTunes and Ibooks for Mac. I then said sync selected books and clicked 2 of the 4. They synced and appeared in Ibooks, The other 2 where not in iBooks, I then said sync all again and it remained at 2 of them 4. I then sync individually another book and it synced.
I also found that in Ibooks library, the sync i did in October I originally uploaded 13 books of which 5 where removed.. If I click in iBooks library on the 8 that did sync then they open in Ibooks, If I click on the 5 that where removed i get a temporary folder that disappears and the book does not appear in Ibooks. Yet originally these books where in Ibooks for mac+ipad and iTunes so surely its not a problem with there particular ePub.They are also immediately removed from iBooks for mac when I do this.
I believe that some point of the chain is failing and then being treated as master so on the next sync they are removed. Its possible my Ibooks simply will do this for every new book I add but I did add 1 book initially.
It seems like I can retain the books by turning off syncing but thats hardly a good long term solution. I am currently testing this