I'm not sure I've seen such VOBs, although I suppose it's possible with several titles or PGCs within those VOBs. Even silent places usually have silent AC3 or whatever kind of audio it is. The audio doesn't just stop. Ordinarily you'd demux the PGCs separately for encoding. But to answer your question, if you just want to encode a bunch of VOBs without regard to PGC (a bad idea in my opinion), then I know of no way to add silence where you say it might be required, and I certainly don't know of any way to automatically find the place that needs it, find out how much silence it needs, and to add it in.
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