The current mixer code in libretro/libretro_mixer.cpp is a copy of a 2013 snapshot of src/hardware/mixer.cpp. I updated it to current SVN of the master branch in order to get bugfixes that have been made to the mixer since 2013.
Before I make a github PR, do you want to keep libretro/libretro_mixer.cpp, or should I delete that file and instead apply the modifications directly to src/hardware/mixer.cpp? This would prevent this code from getting outdated again in the future, but on the other hand could mean upstream syncs could introduce issues.