I use mpeg streamclip to fix the timecodes in merged vobs. I would like a command line utility that does this without having to recode if possible.
Libav has the tool avconv, which allows you to do that with the video filter setpts=PTS-STARTPTS.
I haven't tried this, but the following should do the trick for you:
avconv -i in.vob -vf 'setpts=PTS-STARTPTS' -c:a copy -c:v copy out.vob
For more information you can check out http://manpages.ubuntu.com/manpages/precise/man1/avconv.1.html
You can use this tool I made to fix the timecode without re-encoding, https://sourceforge.net/projects/vob-timecode-fixer/