I did the booking from my account (after logging in online) with my credit card. I received - and still have - a receipt showing that the miles were deducted from my account, the copay from my credit card account. The “helpful agent” told me that her record showed the miles were deducted from my account.
Could it possibly make a difference that I changed the outbound flight and date a couple of days later, paid all fare increases etc., by phone with an agent in some foreign land? But my son’s MP account shows the deduction from his account on the date of my original purchase, so presumptively the itinerary change should have no bearing on the mystery.
Also, my son’s MP number is in my account profile since I have included him as a passenger on many prior bookings.