Conversion creates a new book -- the datafiles which contain annotations and reading position will be inherently wrong, as they are based on formatted character offsets.
There is no need to convert anyway. The PDOC tag is updated on the fly by calibre, just like all other metadata; in fact, calibre's internal copy will
always be set to EBOK, and defaults to switching it to PDOC when sending it outside calibre.
As long as calibre is properly set up to prefer EBOK, all you need to do is resend the book. Do NOT convert it.
Also, make sure the book is using the same metadata/save template, so it matches up with the {ebook}.sdr folder that has the annotations data. If you deleted the book with calibre, it will be deleted as well (don't do that

) if you left it on or deleted with the Kindle UI, it will still be there.