CloudAlly is able to back up and restore OneNote, both from within Sharepoint and within OneDrive.
CloudAlly backs up and restores all content, except for the following items:
- Audio recordings (*.wav files)
- Images created with the Draw menu
- Page color
- Rule lines
- Text styles (e.g., Headings, Normal, etc.)
- Attachments, except for image files, which are restored (Microsoft limitation)