I have several movies that have a stereo AAC audio track, and a multichannel Dolby Digital track. Is there any setting that forces the player to play the multichannel DD track instead of the stereo one? Unfortunately, the stereo is flagged as the default audio track, and I don't know how to change this because these files are MP4 instead of MKVs.
Simple way is to remux into MKV and then you have full access to tracks and their properties. MKVToolNix is your friend ! Then mark the desired track as the default or even remove the stereo track before you hit remux button
I also use the program MKVToolNix. I eventually converted/remuxed all my mp4 movies into mkv. MKVToolNix is pretty powerful tool so you might have to educate yourself on what it can do. To change flags I usually go to the "Header Editor" section of MKVToolNix.
it allows you to queue files up for processing "add to job queue", and then under Job Queue "start automatically" can run all night