Yeah, joining the files together would be wise, since I'm certain when it comes to the authoring step it'll have to change how the VOBs are split up.

As for the audio track, I do not recommend recompressing the AC3 track back to AC3 when you finish editing the sound. AC3 is lossy, and if you recompress the file, you'll lose even more information from the sound file and it'll sound worse (it'd be more noticeable if it's one lossy format converted to another, but the degradation will still be there even if you stick with the same codec). If you must tamper with the audio, please use LPCM when you multiplex it back with the video.


As for what programs to use, that depends on what operating system you're using. I'll leave that part of the question to someone else to answer (unless you just happen to be a Linux user, in which case I'd come in handy).