You need to add every file from every one of your versions to wyBuild. Then let wyBuild do the comparison of your versions. It will automatically detect which files to add, which files to patch, and which files to delete.
Right now you're adding a folder to one version and then neglecting to add it to the latest version. wyBuild sees that as "the use wants to delete the folder in the latest version."
Short answer: add all files and folders from all your version into wyBuild. Let wyBuild do the hard work of making the patch.
Does that make sense?