Despite all of the detail in the OPs post that perhaps shouldn't be public (PNR, case numbers etc), there also seems to be some details that may be relevant but are not included.

Why did you contact the trade help desk, rather than general customer services or Privilege Club? If this was not a trade booking they are unlikely to be able to help you.

Was this a one way ticket AMS-DOH-KUL-DPS, or the return portion of a bigger ticket? And was it a cash fare reduced with avios, or an avios ticket reduced with some cash? And who was operating KUL-DPS and was that a QR codeshare?

And very importantly, were any alternative flights offered and accepted prior to asking for a refund (however inadvertently)? I’m not sure how QR handled KUL flights being switched to being operated by MH but this may also be relevant if your QR flight number was cancelled but the new codeshare operated at the same times and you were automatically rebooked onto that.

The refund in each of these situations can vary, and depending on exactly what happened you may have been subject to the fare rules rather than involuntary cancellation rules, including for the operator of KUL-DPS.

I'm not suggesting QR haven't made a mistake here, but with a little more detail someone here may be able to work out what that was and which department to contact to have it put right.