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Yes, sorry, by notes, I meant not only handwirtten notes, but also highlights, bookmarks, markups and comments.
Actually I've figured where the problem lies. It's a conflict between Calibre and RL - the former, when used for editing mediadata directly on the Reader creates some conflicts, or inconsistencies in xml files and causes RL to refuse to load the reader.
Was cured by simple deleting of all xml files - Reader rescanned the contents of discs and created, new proper files.
Also, this problems seems to be specific to 650 model or new x50 series - I have my old PRS700 - this problem doesn't happen to appear there.
Also, regarding highlights and markups - the rest (actually highlighted text) seems to be located in
D:\Downloads\reader\database\cache\cacheExt.xml file.
But it is yet to be figured out how exactly can it be exported. And I can clearly see that pdf markups are done somehow different - while lrf and epub contain exact quotes highlighted and comments.
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