Lars,
I posted a question today that explains how I go about doing what it is you want to do. What I do is copy the folder structure and source files over to a different drive. Or you could copy it into an empty folder on the same drive. Then I add the top folder, or folders to the batch file conversion window and start the conversion. It works fine, except that it leaves the source files in the folders along with the new files. So you have to go through and delete them. If after the conversion is done you use VIEW in IE to sort the files in each folder by type you can quickly select and delete the source files. But it gets tedious. You have to do this in every folder that contains files. My question was whether there is a way to have the source files automatically deleted. I'm still waiting for any answer on that.