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Actually, I reported "lost css" too, starting after version 6.2. I believe issue #1986 was opened at that time and has never been resolved.
Anyway, the problem seems to happen most often when I import and link stylesheets and then make any change in the metadata editor. Upon exiting the epub, the stylesheets blank out (remain in folder but have no entries).
I've reduced the incidents by linking stylesheets last in my workflow. In any event, I can open the epub as a zip file and drag and drop the missing stylesheets without a problem; they rarely go missing again after the change has been saved.
Strange...but it does happen.
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