Hi Gtrcoop
The only thing I can think of why this did not work - after reconverting the books, you need to remove all your books from the itunes library and then add them again from the newly converted calibre library. That way itunes has links to the corercted metadata and the reverse alpha codes. Then remove them from the ipad and resync as described above.
It seems like a real nusiance to do all this, but believe me, the satisfaction of seeing all your books transfer in the correct alphabetical order (together with the joy of having defeated Apple's insane programming) is well worth the effort.
The real annoyance in all this is that Apple have not issued any real form of ibooks documentation. If there were a reasonable, technical manual available, explaining how sorting is done, then we would not have to resort to guesswork.
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