Thanks for the help, gentlemen. That muxing stuff is way beyond me, I’m totally new to it all but I’ll keep at it.
You can do it directly with ffmpeg without demuxing if you want:
ffmpeg -i 02-ESB_Grindhouse_1080p_BD25.mkv -c:v copy -c:a ac3 -b:a 640k -map 0 02-ESB_Grindhouse_1080p_BD25_ac3.mkv
In fact that’s probably what I should have posted the first time. That’s easy, you can do that.