How do I replace it? I also tried to change the skin of the Droid Marine and remove its rocket launcher (the EPI BD's only had a blaster rifle) but when I munge the map the normal droid marine shows up and none of my changes actually where applied :S I changed the lua's, the odf's and the msh's but nothing really works.
Don't edit those. They are just to look at. You need to create a custom side and load your unit from that. There are many posts about custom sides here on the forums. Search around for them and read the Jedi Creation doc to learn how to create a custom side.