If your goal is just to backup dvds and shrink them to fit on multiple cds/dvds etc, I would use a tool like acidrip or dvdrip to do the job. Both are excellent tools. Pay close attention to the requirements for these programs as that will save a lot of stress. I got acidrip to work first. I had a problem with dvdrip because it would place the perl module in a directory with a different perl version number than I had. But copying the module to the correct directory fixed it easily.
If you are looking to use different vobs from different dvds and remaster, read below.
I was having a somewhat similar problem. I created a dvd from some mpeg files and deleted the mpeg files only to find out that I had screwed up the menus. So, in order to extract the vob files and remaster the dvd, I used dvdunauthor(part of the dvdauthor package http://dvdauthor.sourceforge.net/
). To use dvdunauthor, open up a terminal, cd to the directory you want it to stick the extracted vob files, stick the dvd into your drive, and type " dvdunauthor /dev/dvd/ ", that's assuming /dev/dvd/ is the path to your dvd. If it isn't, simply change it to whatever.
This extracts all the vob files, including the menu and creates a dvdauthor.xml file so you can use dvdauthor to recreate the dvd structure and then burn the structure to disc(I use k3b). If you want to remove or add certain vob files, just edit the xml to reflect that. Of course if you change things and want a menu, you will have to rebuild the menu vob file(do this with dvdauthor). There are several excellent guides linked from the dvdauthor site on using dvdauthor to create menus and the xml file for dvdauthor. A head's up on the menu creation though, imagemagick changed the way it handles transparency and so you need to patch the dvdauthor source or disable the use of imagemagick in it, otherwise it will have a problem creating the menus. Just google the patch or the exact line # to change. I think I found the patch on a mailing list and the line #for disabling imagemagick on a place called the Hacker's Corner. I'll look for the links and post them here later.
This is my understanding of the issues and processes, if anyone else sees something I stated incorrectly, please reply with the corrections. Hope this helps.