Well, ideally the textual contents of the two files would be the same (being the same ebook), so locations wouldn't change.
If I could take a look at the internals of how Amazon store highlights/notes I could already answer many of these questions myself.
(edit)
I've seen that Kindle devices create a MyClippings.txt file within their file system, but I don't know if this is where highlights are actually stored or a mere exports thereof.
(No isbn/asin/id in there, so I'd opt for the latter.)
Last edited by atava; 12-25-2017 at 01:07 PM.
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