It is my understanding that if you fly on AF-KLM flights (flight number coded under AF or KL but either operated by SkyTeam or Non-SkyTeam) if the miles is to be credited into FB account, it should be counted towards level flights and miles (this will not work if flights are to be credited into other SkyTeam programs). But with all the changes and confusion with FB since June, my understanding on this could turn out to be a complete misunderstanding.

I am with the OP that since the flight was coded under KL flight number and therefore, it should have been credited properly with level flight and mile into FB. Let us know whether you get this clarified by KLM. It is worth to try as one of the posts here says though, claim the missing miles online using KL4102 and see what it says. Who knows, you might end up getting mileage credit on both flights, KL4102 and MH 016.

I strongly believe "DL coded share flights" with China Airlines (CI) and other non-skyteam partners earn full elite miles as long as the flights are coded under DL, tickets are purchased through DL and miles are credited into DL account.