I'm encountering a bug where some books are never recognized as up-to-date with the update mode set to "Overwrite if Newer". Even if you just downloaded/updated one of these books, attempting to update it through FanFicFare will fully re-download the book instead of immediately stating after retrieving the metadata that the book doesn't need to be updated because the website isn't newer.
I've narrowed it down to almost all of my books in my library from archiveofourown.org and fimfiction.net that were updated in the current year (2019). Older books from those websites and all books from fanfiction.net, spacebattles.com and royalroad.com don't have any problems.
Here are two example fanfics where this is occurring, one from each website:
https://archiveofourown.org/works/17960324
https://www.fimfiction.net/story/426519/
The metadata for each problematic book shows the latest packaging date under Date correctly. Deleting a problematic book entirely and redownloading it using FanFicFare doesn't fix the problem, nor does uninstalling and reinstalling Calibre.
I've tested both Calibre v4.1.0 and v4.2.0 on Windows 10 and I'm using the latest stable release of FanFicFare.