Okay, apparently the configuration object used during Calibre update is a 'lightweight' version. 'Lightweight' config/adapters are used for internal stuff only and don't generate any network traffic.
For reasons I don't remember, that includes not setting up to use the storyUrl section.
I'm looking into it to see if that can be changed. It's pretty non-intuitive as-is.
In the meantime, you could use a replace_metadata line conditional on storyUrl or storyId instead of story URL section.
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