The LZW compression I wouldn't think would change any headers in the file and is lossless, but that's a good point and I'm sure they'll test the files out.
As for the command line, looks like the process of doing multiple files is left up to the shell so windows command like psyang says or bash equivalent or whatever.
You could also morgify them, then you don't end up with a copy.
http://www.imagemagick.org/Usage/basics/#mogrify