Ah, that should be easy enough to fix. In fact, here you go, updated version of the command prompt extractor XD Also it now adds an underscore to the end of the file name if it already exists. It was kind of a lazy solution though, so it's added RIGHT at the end (after the extension), so you'll probably have to rename it. It's just to avoid the first file being overwritten.
Anyway, I'm not 100% sure if this'll work or not, since I haven't downloaded any of the big ROFs yet, but it should be fine
I wonder if this topic would be better in General Oddworld Discussion? Just because it doesn't seem to be really getting noticed here and this is pretty awesome stuff you're doing.