$s='BS0001/BK0003,或者 BK00006,或者 BK00006/BBM0009/DDK0003';
preg_match_all('#([^/\s]+?)/#s',$s,$m);
print_r($m[1]);

/*
Array
(
    [0] => BS0001
    [1] => BK00006
    [2] => BBM0009
)
*/

------解决方案--------------------

PHP code

$str    = "BS0001/BK0003,或者 BK00006,或者 BK00006/BBM0009/DDK0003";
echo    preg_replace("/.*?\b([\w]{6,})[\w\/]*/i", "\\1,", $str);

//BS0001,BK00006,BK00006,