As far as i know somewhere mentioned about auto-update. You better to use steam auto-update. Not experienced steam-auto-update bugs such as yours so try to follow that way. (or follow the hint above, all the downloaded files wont be deleted so you can simply install the game in the same directory and not be scared of losing files)
Did you run auto-update with the steam version? That shouldn't even be possible anymore.
If not: I can imagine that CS2D doesn't allow to update these files as CS2D is using them and the auto updater is basically just another instance of CS2D.exe launched with some special params... hmm.. that's a problem indeed. Would probably have to ship the game with a small dedicated binary for updating then.