Here's a secret trick to restoring Reference-samples to the pristine shape.
1. Inside the Jupyter file navigator, click "New -> Terminal"
2. In the terminal, run the following commands:
rm -rf ~/Reference-samples rm ~/.jupyter/.staging_complete
3. Restart the Jupyter server (click Control Panel, then Stop My Server, then Start My Server)
Once the Jupyter server restarts, you should have a pristine copy of the reference samples in your home folder.