It is hard to know exactly what happened.
First, CC has always downloaded metadata if the metadata in calibre is newer than the metadata on the device. By "newer" I mean calibre's last_modified date is newer than the last time metadata was downloaded. If the fanfic downloader touches metadata, for example updating a custom column, then the last_modified date will change and CC will download that metadata. The modified date for books plays no role at all this decision, and never has.
You say that you sort in CC by date. Which date is that?
It sounds like you want to know if the book (not the metadata) on your device is older than the book in calibre. There is no way in CC to check this. Others have asked for it, and it is on the wishlist. The problem is that it is likely to be slow, because checking the dates on files requires going to the actual files on the disk. I am still looking at how this might be done.
One way that some people use to get around this problem is calibre's reading list plugin. That plugin can automatically send books to the device on connection, ensuring that the metadata and the books match for those books. I think that the fanfic plugin has some kind of connection with reading list for exactly this reason. Reading list can handle updates to more than one device, but I don't know if the fanfic connection (if there really is one) can update more than one reading list.
I know that there are other fanfic people out there who use CC. I will change the thread title in hopes of attracting their attention so that you can converse with others of like mind. And I might learn something.
