In DVDAfterEdit 3, the name of the folder which encloses the VIDEO_TS folder is very important, as is the contents of that folder.
First of all, that name is used to create the project file, and unfortunately the program currently does not distinguish between the same folder names at different levels of the disk hierarchy. This will be fixed in HDAfterEdit, which uses full project files and non-destructive editing.
The enclosing folder name also becomes the name of the DVD Video disc when it is replicated. And all folders and files within this enclosing folder (at the same level as the VIDEO_TS folder) become the ROM data, for disc images as well as replicated DVD's.
If a mistake is made in building a VIDEO_TS folder to a bad place and then it is opened in DVDAfterEdit before moving it to a better place, you should delete the project file to prevent further errors. To do so (See Project Files):