Exporting and importing notebooks through OneNote for the web is only available for notebooks stored on personal OneDrive accounts, not for notebooks stored on OneDrive for Business or SharePoint. For information about exporting notebooks to PDF files from OneNote 2016 for Windows
Not extracting one notes to PDF!
Use eDiscovery in the compliance Center to search for .one files in Sharepoint and export them via here. You can then go through the import process via the application