[Adoby]

Unfortunately I don't think that calibre deleted the books without your intervention.

It isn't impossible, but highly unlikely.

I think it is much more likely that you caused the problems when you stored the calibre library on a NAS, or possibly when you moved the library to or from the NAS. There are for instance well known problems with using the calibre library on a networked filesystem and on operating systems that have different case sensitivity. If you ever did some work on the library from a Windows computer, that might have been the cause. Or if you used SMB or CIFS on the NAS. One symptom is exactly what you described. The books are listed in the GUI, but when you try to access them they seem to be missing. Another cause could be that you have changed the files in the library using some other tool than calibre, and then inadvertently made some minor change in the filename. Unfortunately, there can be quite a while between whatever you did that caused the problem and you discovering it, so even backups may have the same problem.

I have successfully stored my calibre library on a NAS, but I used NFS, not SMB or CIFS. And I once updated books from Windows, and experienced your symptoms. I was able to restore everything without problems. The books were there, just with the wrong case in the paths and the filenames.

Usually the books are not deleted but remain as abandoned "orphans" somewhere in the calibre library. They are different from what is stored in the database, or stored in a folder with a different name, so calibre can't recognize them. Perhaps with a slightly different name. But if you have copied the library from one system to another you may have inadvertently deleted those orphans, that wasn't copied with the rest of the library.

One way to check is to use the calibre database maintenance functions. Check the library. Another is to simply move the library to another folder using the calibre GUI, and see what files remain in the old calibre library folder. All on a local filesystem of course. It may even be possible to use the maintenance functions to fix the problems automatically, if you are really lucky. It might be a good idea to backup the calibre library before you try to fix it. That way you can be sure not to loose more books.