It's not the easiest thing in the world to achieve, but yes, TMPGEnc DVD Author can be used for this.
I've done it three times on DVDs created by DVDSanta, where I just wanted better chapter control and menus.
Start a New Project and select Add DVD Video to load the movie from the DVD. There is an option to remove current chapter markers while loading.
It's also best to copy the DVD to your hard drive before loading. Processing is much faster.