Comment by diath

I had that happen when somebody tagged me in a private repository that was later deleted (?).

You can fix it through the API by generating an API token in your settings with notifications permission on and using this (warning: it will mark all your notifications as read up to the last_read_at day):

    curl -L \
    -X PUT \
    -H "Accept: application/vnd.github+json" \
    -H "Authorization: Bearer <YOUR-TOKEN>" \                            
    -H "X-GitHub-Api-Version: 2022-11-28" \
    https://api.github.com/notifications \
    -d '{"last_read_at":"2025-10-09T00:00:00Z","read":true}'