See the FAQ
Do not put your calibre library on a networked drive. You have likely corrupted your library. The missing document files might still be there but with the wrong calibre ID.
I suggest you:
- move the library to a local disk.
- run calibre's check library tool to see what damage you have.
If check library finds "extra titles" then these might be your missing PDFs. You can recover them by adding the PDF to the calibre entry with the metadata but without the PDF file.
And please (!) don't tell us "But I have been running on a NAS for years without problems." We hear that too many times from people whose library is damaged.