Finally someone who is looking into that !
I’m trying as well to replace musics in pokemon Y
Apparently, loop points are stored in the .bcsar file in the sound folder, but after extracting it I don’t really think it’s there
I tried replacing a music without adding something, and the game crashed (second time, the game just didn’t have any music playing)
Also, apparently no one tried to look into that (couldn’t find a thread or something about that)
EDIT: Apparently, the bcsar contains only battle sound, sound effect and maybe some pokemon cries template, but nothing about looping points
EDIT#2: I found 2 channels (PlatinumMaster and recordreader) both have successfully replaced music in CY, and apparently PlatinumMaster will post a tutorial on that