Tried all kind of encoding, but output file has not changed. So I think encoding option is not working at all. (I tried also korean / japanese codepages / cyrillic (russian) / slovak-czech ISO, LATIN, CP1250-1-2. Output file was no changed.
Maybe I am doing something wrong... In preferences > Common options > Input character encoding I am trying to set encoding (for example cp 1250 (which worked in my older Calibre version, unfortunately I dont know version number)) and then I set bulk conversion for 2-3 books. The books looks the same no matter what conversion I set.