Take a look at http://www.mobileread.com/forums/sho...d.php?t=196946
for some ideas on conversion via command line.
You want something like
At command line
for /r %1 in (*.epub) do "c:\Program Files (x86)\Calibre2\ebook-convert.exe" "%~dpn1.epubi" "\my\output_directory\%~n1.mobi"
This will convert all epubs in the current directory and all directories under it to mobi's and place them all in \my\output_directory.