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Windows and Linux filesystems has different case sensitivity. Your Synology NAS use a variant of Linux, DSM.
In Windows the files: "BookTitle.epub" and "booktitle.epub" are the same files.
In Linux the files: "BookTitle.epub" and "booktitle.epub" are two different files.
Same with folder names...
So when you copy or move your library and update metadata, fix spelling and title/author leading UPPER/lower spelling, and so on, you may slowly cause increasing corruption in your calibre library. Weird errors with missing formats/files or books and extra duplicate or orphan folders and books.
I stopped using Windows and Samba/CIFS to access my calibre library on my Synology NAS and instead used Linux and NFS. Now I have no problems. I only access my books on my NAS from either a laptop or a desktop PC, but never ever simultaneously. I assume other NAS brands have the exact same problem.
To fix your problems I suggest that you use the functions in calibre to MOVE your library back to your PC. Then check the folder for the old library for orphan books and add them to your libarary. That way you should not loose any books. You may have duplicates if you fixed "lost" books before...
Then use your NAS only to make backups of your calibre library. Or convert to Linux and NFS...
There may also be some settings to the Samba/filesystem configuration on the NAS that also might fix this, I never researched that.
Errors in calibre due to different case sensitivity in filesystems are often delayed. Meta data changes to files and filenames are not written to calibre library at once, just stored in the database. Later, perhaps after weeks, months or years, when filenames for books are updated for some other reason, some files and or folders may go missing and/or are duplicated seemingly at random. Very strange errors if you don't realize what is going on.
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