[atava]

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.)