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I filed a GitHub support issue about this and got a response with a pretty good workaround:

The curl command below will mark all of your notifications as read and, with any luck, will take care of that phantom message for you.​

curl -X PUT
    -H "Accept: application/vnd.github.v3+json" \
    -H "Authorization: token $TOKEN" \
     https://api.github.com/notifications \
    -d '{"last_read_at":"2022-05-31T00:00:00Z"}'

A few things to note:

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Bug GitHub or a GitHub feature is not working as intended Enhancement An idea, feature request, or improvement to a GitHub feature Notifications Keep track of everything happening across all your projects General General topics and discussions that don't fit into other categories, but are related to GitHub Product Feedback Share your thoughts and suggestions on GitHub features and improvements