I'd do as Duffer suggests. I've always had a lot of issues with wadupdater and easywad (wrongs paths, several copies of the same file, that sort of thing), maybe because i never understood what they're supposed to do, while WadController works as I think it does.
A global advice when working on tracks / cars: always rebuild the wad from scratch for a folder on your drive. It's much easier to maintain a clear archive, as the contents of the folder you work in are the same as the wad file.