I know the thing is in beta, but I opened up a custom map, and just hit the save button in your editor. Didn't change a thing. Then I reopen it in WorldEdit, and all the rifleman are bandits and all the barracks are towers =P
No no no! You had a good idea to tell me that! That's really interesting since I'm not "touching" the units part right now. I jus modify the players info in the ".W3i". I really appreciate that you send me your map before and after saving, or just before (I can save by myself). Let me know if you've got other weird bugs of this kind!