Wish you had written about your audio problems – all was not lost even if you picked the wrong audio track. Here’s how to proceed if you do this again.
First of all, let’s just get some understanding here. If we pass through an audio track, no matter what kind, all we are doing in Handbrake is re-encoding the video. So the only stream that is of any import to us at that stage is that video track. We really don’t even need the audio track then.
To add (or change) the audio track later is easy. First of all, you’ll need to strip it out of the original file, so a program like tsMuxer is used to demux the track in question (and one of the options for that is to take only the core of an HD audio track. The Live can’t play a DTS-HD file, so it’s the core we need. And the Live doesn’t play True-HD in an MKV container either, so the AC3 core of the True-HD is all we need there as well).
Now that you have the audio track separate, you can remux it back with the Handbrake encoded video file using a freeware tool like mkvmerge. In this case you’d load up the Handbrake MKV file, remove the Handbrake audio (the wrong one) if need be, and add the demuxed audio track from txMuxer, and then make the file.
The advantage to all of this is that the real time needed in encoding is all video – so if you’ve spent some hours in Handbrake getting your video right, it will only be a matter of minutes to both strip out the audio track you need AND put it back to an MKV container. So – a little complicated, but saving many hours of time.
As to the nightlies, here’s the link:
While the warning about using them sounds ominous, most experienced Handbrake users are indeed using them with great success. As with the major rule in life, we don’t want to fix something which isn’t broken, so if you are having no issues using Handbrake then don’t worry about it. However, if you come to a blu-ray which doesn’t work for some reason, the first thing you should try is one of the nightlies (in particular a blu-ray encoded with VC-1 doesn’t work with the release version, and you will come across these soon if not sooner).