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  • Contact GitHub Support, explaining the issue clearly—that you’re seeing an unread notification for a repository that now returns a 404 and can’t be dismissed by the UI. This was solved in #82108

  • Run the API command below in terminal to mark all your notifications as read instantly (this eliminates the lingering dot):

export now=$(date +%Y-%m-%dT%H:%M:%SZ)
export TOKEN=<YOUR_PERSONAL_ACCESS_TOKEN>
curl -H "Authorization: bearer $TOKEN" \
     -X PUT \
     -H "Accept: application/vnd.github.v3+json" \
     https://api.github.com/notifications \
     -d '{"last_read_at":"'"$now"'"}'

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Answer selected by wolfsilver
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Bug GitHub or a GitHub feature is not working as intended Repositories The core of version-controlled code storage
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