Why not use calibre but strictly from the command line?
See
http://manual.calibre-ebook.com/cli/ebook-convert.html
For instance, I just typed
Code:
"c:\Program Files (x86)\Calibre2\ebook-convert.exe" unixfaq.mobi unixfaq.epub
and did a conversion from mobi to epub and did not store anything in it's database, and could put the files where ever I wanted.
And there were no extra copies of anything made either.