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Sorry if this has been mentioned before...When I open a pdf in calibre ebook viewer the highlighting experience is very different from the main Calibre program. The ebook viewer has the new highlights and annotation tools; the main program doesn't. Is this true only for pdfs?
The ebook viewer creates a new copy of the pdf with the annotations and highlights and leaves an intact original. Good idea but some sort of file name change might help the user.
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