Not that this will help, but award and bonus miles for upgraded classes are documented with a comment line that seems to make no sense to the common eye, in the reservation computer in the PNR. That's the only line that governs the accrual of miles and how much bonus is given.

I'm thinking this is a fairly automated process, so I don't know what happened. I'd shut up though

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When once you have tasted flight, you will forever walk the earth with your eyes turned skyward, for there you have been, and there you will always long to return.

- Leonardo da Vinci