Conversion will create an entirely new book as far as the annotations are concerned. It completely changes the internal css and html markup, which is use to find the file offsets that identify annotations.
It is also unnecessary. calibre does not change the cdetype when converting -- the PDOC tag is added when you click send to device. Since you changed that setting under MOBI Output, it should preserve the EBOK tag. Just resend the book and it will be fixed.
To preserve annotations, make sure the resent book overwrites the old book. It must be saved to the exaxct same file location. Then the annotations files will match up to the book.
Last edited by eschwartz; 04-27-2014 at 12:28 PM.
Reason: typing-on-a-kindle-touch typos
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