In my experience, installing Anaconda seems to be related to the issue. Upon creating a new user profile with neither application on it, then installing ArcGIS Pro, it worked fine.
However, I recently installed anaconda again and now I am encountering the same issues. In addition to the jupyter notebook problem, there are several tools such as summarize within and apportion that will not work any more.
It would be great if we could figure out how to fix this without having to create a new user profile; uninstalling both Pro and Anaconda and deleting all related directories, does not seem to work.