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Newer Kindles (from the Kindle Touch and on) handle annotations using a {bookname}.sdr folder next to each {bookname}.azw3 file. The {bookname}.sdr folder must have the same filename except for the extension, and inside the "sdr" folder you will find the *.(azw3r|azw3f|apnx|mbp1|mbs) files.
As long as you copy over the ebooks and the annotations files in the same folder structure, your annotations should transfer over seamlessly.
Older Kindles, e.g. the Kindle Keyboard, stored the annotations in a *.mbp file I think. Also, they weren't kept in the "sdr" subdirectory.
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