This is a pretty big problem. Amytime I update a plugin (icluding buddypress) .mo translation files dissapear - magically!!!
I have those files for a bunch of plugins on my computer and this saved my ass a few times... .
Now maybe WordPress itself, won't check for any files when updating a plugin, but is there a way to provide plugin developers with a feature to check for any .mo language specific files and avoid removing it upon update? Or at least ask the user before removing any files "The following files will be vanished! Do you want to continue?"