[chaley]

You seen to say that some files contain internal links to the uppercased filenames, which are missing. Calibre might be resolving that problem by copying the lowercase-named version to an uppercased version, with the goal of making it work on a case sensitive filesystem.

Try searching the files for links to duplicated files, that is links to the uppercased version. Change those links to point to the lowercased version, thereby making the collection of files internally consistent.