I find that difficult to justify, and wonder if the FB agent was merely trying to draw a line under the affair - signaling their unwillingness/inability to advocate for (partial) refunds with the partner airline in question - or instead encourage you to rebook which you appear to have gladly (and wisely) done.

That said, it is not in any Flying Blue agent's power to override or "fix" any such mistake made by a third-party, non-alliance partner. It would be up to the pax to deal with the partner in question, so what the FB agent told you was probably in practice true, even if in reality it should not be true.

Given that it's MH who decided what to charge, on a ticket with apparently no inherent baggage allowance, I really think the OP will struggle to get anyone at MH to even look at this case again. And it's not up to Flying Blue, or KLM, to refund MH's baggage fees.

To the OP: KL flies to KUL, at least on some days of the week. Next time, beware of the pitfalls of booking Light tickets that include non-alliance partners - whether or not they are coded as KL or AF flights. You have no Skyteam benefits as regards extra luggage on such flights.