Hi again, Version 0.4 (20090312) is uploaded: http://wiki.lyx.org/Tools/ELyXer Direct link: http://wiki.lyx.org/uploads/Tools/eLyXer/elyxer-20090312.tar.gz It now ignores ERT, and supports footnotes, newlines, bibitem entries and citations. If you are interested in living on the rough frontiers of command line tools please give it a spin.
Thanks, Alex.