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... I mean that FFDL can set and update the calibre metadata for stories from the websites they came from?
FFDL has several 'Update' modes. In 'Update EPUB if New Chapters' and 'Overwrite if Newer' modes, FFDL will not update the calibre metadata unless there are new chapters, or the story on site shows a newer date, respectively.
The default (and most useful, IMO) is 'Update EPUB if New Chapters'. If there are new chapters available, it will download only the new chapters, add them to the existing chapters, and then update calibre's metadata. (I recommend all users download to epub for that reason and convert if needed.)
If you just want to update your calibre metadata for a story, there's the 'Update Calibre Metadata Only' mode. Generally, unless there's new content for the story, the metadata hasn't changed either. So I really only consider that useful occasionally--like if you're adding new columns to your library.
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I would point out that I discourage using FFDL to check for story updates. I 'workflow' I use--and suggest FFDL users use--is to subscribe/follow/favorite/alert/whatever your stories on the various websites and only update them in calibre when you receive email notices that they've been updated. We've seen cases where sites will block you if you hit them too often too quickly.
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