Upgrading by miles is a tricky issue for JL mileage bank.
I asked JMB customer service 'Can I credit miles to JL when CX D class is upgraded by CX miles to first class (booking Z)'.
JMB answered 'Z' is ineligible for crediting to JMB by mail (e.g. not oral communication). In this case, they say they can not credit miles based on the orignal fare (D).

Of course, they may be wrong.