I used SpamAssassin (and BogoFilter and couple of others as well), always with duplicating. It is quite unclear when that bug 138846 was marked as resolved, moreover it has been marked as a duplicate of another bug (which looks more generally), also marked as resolved, which then has been marked as duplicate of one more bug, but this one is in Unconfirmed status. Anyway, I don't know, where it has been resolved (if it really has), but my kmail duplicates with all filters which somehow modify mails themselves, should it be SpamAssassin or Bogofilter or any other.