Okay, I think I got FLAC working with HD-DVDs' DD+ soundtracks. Again, many thanks zgx for the guide.
1) Use EVOdemux.exe to demux the desired DD+ audio track.
2) Use EVOdemux.exe to rebuild an EVO that ONLY contains the desired video stream.
3) Use the previously posted instructions to create an MKV file, using GraphEdit, Haali Media Splitter, and Haali Muxer.
4) Use Sonic Audio Decoder 4.2 in GraphEdit to Dump a (huge) .raw file onto your hard drive (look at previous posts on how to do this).
5) Use Sox to convert this into a .WAV file (again, look at previous posts - just make sure to use the -3 option). With DD+ this should result in a 24 bit multichannel WAV file.
6) As per zgx's instructions, convert this to flac with MediaCoder (so far as I can tell, you do NOT need WaveWizard. When I used WaveWizard to remap, it seemed that the center channel got remapped to the left rear speaker! I hope someone can confirm this for me.)
7) Use MKVMerge GUI to mux in the flac stream into a new MKV.
Now, surprisingly, I did not need to figure out the audio delay. I had to do this before, when I was encoding to AC3, but not this time! I don't know why - maybe the encoder I used ignores silence? Anyways, this is a good thing - makes things simpler!
If you use FFDShow Audio Decoder, make sure that FLAC is enabled in the codecs settings.
Enjoy!
For reference, I used the Harry Potter Goblet of Fire HD-DVD. The re-encoded 640kbps DD5.1 soundtrack was ~730MB, which is exactly the same as the DD+ soundtrack. The FLAC lossless soundtrack takes up 1300 MB of space. Pretty good!
Naturally, the FLAC/DD+ soundtrack sounds far better than the AC3 one - because I used FFDShow to create the AC3 one, which isn't very good - the volume was too low!