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FYI, the fanfiction downloader for mac that Rika24 mentions is unrelated to FanFicFare. It is, in fact, why I changed the name of the program I maintain.
I don't know if FanFicFare will be able to update epubs you've already downloaded using the fanfictiondownloader.net tool--I've never tried. But FanFicFare will only try if you tell it to, and it won't do anything to stories that it can't find online.
So while there's no risk of losing stories that have disappeared entirely, if you attempt to update a story that you've edited or that the author has removed chapters from you could conceivably lose some content when FanFicFare re-downloads chapters or discards chapters the author deleted online.
(Sorry for the late response, I didn't see this thread before.)
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