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One interesting thing that Amazon did out of necessity is come up with a way to have highlights and annotations be transferrable between copies of a book in different formats. They needed to be able to do that in order to have highlights work for customers owning a variety of devices that might be used to read the same book in MOBI, KF8, AZK, KCR, and KFX formats. Each of those formats have their own method for identifying the position of text within a book.
As far as I can tell they do it by building a file for each format that maps plain text to that format's positioning system and then matching the text between formats to find the corresponding position identifiers across formats.
The same technique can also be used to map positions from the current book content to a new revision when the publisher updates the book to make minor changes or fix typos. That allows the book to be updated while keeping highlights/annotations in the correct place.
It would be interesting if someone came up with a similar method to map annotations between different reading platforms. It would take a lot of research and work to accomplish.
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