I'm really late to the party, but I found this when I was looking for a way to NOT go through what I ended up having to do. 
I wanted to be able to listen to Spotify and play Pokemon Y at the same time. So I extracted a cci, built with ffmpeg a aac file of 120 seconds of silence, and ran a powershell that replaced all BGM_xy_***.aac files with the aac I created with ffmpeg, but have my new aac be named the exact same thing.
Now I have a game with all Pokemon cries (crappy though they may be), all jingles like healing or getting item, button click sounds, attack sounds etc, but no annoying music that can't be turned off.
I wanted to be able to listen to Spotify and play Pokemon Y at the same time. So I extracted a cci, built with ffmpeg a aac file of 120 seconds of silence, and ran a powershell that replaced all BGM_xy_***.aac files with the aac I created with ffmpeg, but have my new aac be named the exact same thing.
Now I have a game with all Pokemon cries (crappy though they may be), all jingles like healing or getting item, button click sounds, attack sounds etc, but no annoying music that can't be turned off.
