I have made it to level 5 mastery on the Harrier GR9, The game allowed me to put a new skin on it and upgrade the weapons pack, but whenever I fly it on a mission, it reverts to the basic setup. I purchased the reward which says that enemy flares won't work against my hat seeking missiles yet every plane I shoot them at successfvully deploys flares. What am I doing wrong.
I have reached level 27 so far, and have experienced the same difficulty that you have. Somehow, the weapons upgrade in terms of the flares, enhanced guidance for missles etc, only seem to work on online deathmatches.......That is what i have experienced.
Hope this solves the dillema