Wait a minute, this is probably the problem. I am so used to doing this that I totally forgot I do (and that others don't):
All your Kindle book features are created by using a special sidecar folder in your documents folder.
Your book is saved as %Kindle Drive%\documents\{book-title}_{asin}.azw3 which I shall assume is Drive E, so that would be:
Quote:
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E:\documents\The Name of the Wind_ The Kingkiller Chronicle_ Day One_B0010SKUYM.azw3
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The sidecar folder (.sdr) would therefore be:
Quote:
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E:\documents\The Name of the Wind_ The Kingkiller Chronicle_ Day One_B0010SKUYM.sdr\
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See Attachment for a screenshot of what this folder looks like. As you see, there is an author file,
an x-ray file, the .phl archive which contains public highlights, the azw3r and azw3f which have notes/highlights and current reading position and the .apnx file with the pagenumbers.
These file/folder names must match up for the Kindle to recognize the appropriate sidecar to your book.
You will have to rename the file to match this folder. By default, calibre saves it as (relative to E:\documents\) : {author_sort}\{title}\{title} - {authors} which will look like (unless you renamed the book while in calibre):
Quote:
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Rothfuss, Patrick\The Name of the Wind: The Kingkiller Chronicle: Day One\The Name of the Wind: The Kingkiller Chronicle: Day One - Patrick Rothfuss.azw3
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I take care of this all by adding a custom column to calibre called {#origfile} which contains the original filename, then use a custom save path to make calibre automatically save with this filename if available. If you like, I can guide you in setting all this up.