If you hadn't upgraded, it might be possible to do this by not entering a mileage plan number at all during travel, and then submit boarding passes to the different airlines for retroactive credit.
However, since Alaska already has your number in the system for the upgrade, it is more complicated. Since AS doesn't seem to know, I'd recommend calling NW to see if they have an answer. If there is no established protocol, it might be possible, but difficult, to get the two programs to coordinate on this.