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:
For more information you can check out http://manpages.ubuntu.com/manpages/precise/man1/avconv.1.html