Clone DVD will not work with HD DVDs. It requires standard definition dvd-video as input.
If you want to convert HD DVD to standard definition dvds, it will require a little bit of work. First rip the movie to the hard drive.
Use ClownBD to select the main movie and output as an M2TS file. Audio can be problematic. Many HD-DVD's and Blu Ray movies have audio encoded in forms or bitrates that are incompatible with dvds. So if you have an audio stream that is already AC3 at 448 kbps or less choose that. If not, convert the audio with ClownBD to AC3 at 448 kbps or less.
So now you have an m2ts file with audio compatible with dvds. You can import this into AVStoDVD and convert the video over to dvd standard definition and produce a finished dvd-video ready to burn. I strongly advise not setting AVStoDVD to burn automatically with this type of input. You need to check the results before burning to a disk.
Once you are sure the dvd works properly, you can burn to a disk with ImgBurn.
Guide for ClownBD: http://www.mediasmartserver.net/wiki/index.php/Clown_BD
I've done this process with Blu Ray input, but not HD DVD. If you run into a problem let us know, and we might be able to help.