eac3to does it just fine for BluRay ==> Command-line : eac3to input.file+input.file.2 trackno: output.file -options trackno: output.file -options (for the chapter track, it's a text file)
For HD-DVD, I know I've done it before but can't remember if it was done with eac3to to (applied on the .EVO Files) or directly with EVO-Demux.
I can't check right now because I'm at work and don't have the hand on my home PC, but if you can't make it work, just PM me, I'll look into it and post the answer.
PS: For eac3to info =>
http://forum.doom9.org/showthread.ph...ghlight=eac3to