Eu tentaria consertar os nomes dos arquivos com convmv - não tenho certeza se está disponível para Windows, o Ubuntu tem em repositórios. Esta é uma ferramenta que usei para esse caso de uso exato. Do seu manual :
convmv is meant to help convert a single filename, a directory tree and the contained files or a whole filesystem into a different encoding. It just converts the filenames, not the content of the files. A special feature of convmv is that it also takes care of symlinks, also converts the symlink target pointer in case the symlink target is being converted, too.
All this comes in very handy when one wants to switch over from old 8-bit locales to UTF-8 locales. It is also possible to convert directories to UTF-8 which are already partly UTF-8 encoded. convmv is able to detect if certain files are UTF-8 encoded and will skip them by default. To turn this smartness off use the --nosmart switch.