The following terminal command will recursively convert .EPUB books in the current directory to Kindle MOBI format. The original files are kept. The ebook-convert program is part of calibre package (in Ubuntu and similar, run sudo apt-get install calibre).
find . -name "*.epub" -exec ebook-convert {} {}.mobi \;
find . -name "*.epub.mobi" -exec rename 's/\.epub\.mobi$/.mobi/' {} +
Thanks! Worked!