Put your language files to a place where they are not overwritten. Then change the path to your custom language files on 'load_textdomain_mofile'
.
Pseudo-code, you have to change the path and the text domain:
add_filter( 'load_textdomain_mofile', 'wpse_63643_custom_eo_lang', 10, 2 );
function wpse_63643_custom_eo_lang( $mofile, $domain )
{
if ( 'eventorganiser' === $domain )
{
remove_filter( current_filter(), __FUNCTION__ );
return '/full/path/to/your/language/files.mo';
}
return $mofile;
}