I'm not completely sure I understand you correctly. On the Led DVD there's probably a menu where you choose between PCM, DTS and AC3, and its default is PCM, right?
Now, when you do a full-disk copy but only take the AC3 track with you, you think it won't play with sound, right? I take it your example is only theoretical and you haven't yet tried it.
Here's how I think it works:
The menu is programmed to assign every checkbox to an audio stream, e.g
1st box (PCM) -> Audio Track 0
2nd box (DTS) -> Audio Track 1
3rd box (AC3) -> Audio Track 2
Now, if you leave out PCM and DTS, your AC3 stream becomes Audio Track 0. Therefore, either your DVD player recovers gracefully and just takes the only available track or it may even crash/freeze. If that's the case you'll just have to choose the checkbox that corresponds to Audio Track 0 (in our example: 1st box).
To your question, I haven't heard of a movie that had problems with "missing" audio tracks. What can and does happen is that certain audio menu items won't work.