I'm not quite sure what you're trying to do. If the problem if that you don't want to store your old versions, then you can just create a single version tab in wyBuild and that will update any version. The downside to that method (single version tab, instead of a tab for every version) is that wyBuild won't generate patches. That is, it will use full files instead of generating tiny patch files.
Does that help, or have I misunderstood you?