Hi Fujiko，
We have found the reason and fix the vulnerability with MacOS. You will receive an update 3.6.4 recently.
Hope Disk Drill could help you got back your PDF files. And you could re-link your notes with the PDF under this instruction: Recovering files in a Mindmap Notebook
Every note in MarginNote is like PS layer on the PDF. These kinds of notes layer are separated in Doc notebook and Mindmap notebook. All of them is saved safely in MarginNote SQL database, which is different from PDFs. Furthermore, if some of your notes are Doc notes, you need to use a new Doc notes re-linking tool of 3.6.4 to get your notes back to your PDFs. If you have any trouble with notes data, the support team could help you.
NOTE: Disk data recovery needs to be done the sooner the better.
Regards,
Lanco