Until it is resolved, here's the method I use to update my existing fics. It's a bit tedious compared to just downloading the ePub and replacing it, but it preserves the FFF structure and FFF is able to recognize it for further updates.
1. Download
FanFictionDownloader.
2. Open it. Set the download folder if you'd like. Paste in your ffnet url and click "check."
3. Once the info pops up, set it to download only the last chapter, and use HTML output.
4. Download the chapter.
5. Open Calibre and find your fanfic. Open it in ebook-editor.
6. Use File > Import files into book to import your HTML file.
7. Rename it to be consistent with the rest of the files. (This seems to be key to FFF detecting it properly in the future.)
8. Manually update your title page and ToC (Tools > Table of Contents > Edit ToC). Delete the title page info at the top of the imported file and fix any other formatting you'd like.
9. Save the file. Edit your Calibre metadata manually.