First I would use a DVD copying program. Maybe your DVD drive or system came with one? Look for Nero or RealDVD. There are also some on the net.
Second, I think you can use Encore, though I have never done it. In the build menu, one of your choices for the ‘Source’ is ‘DVD Volume’. Try pointing to your DVD drive and see what it does. You may need to copy the files from the DVD to the hard drive if you want to write back to a DVD.
Next, you should be able to pull those .m2v and .ac3 files as assets into your timeline. You will likely need to re do your chapter points and menus, but it should allow you to replicate the disk.
Finally, and as a lesson learned, I always output to a DVD Image. I have a hard drive full of images (and backed up, of course). Encore lets you build DVDs from images.
Pauley