For those wondering what became of this (I am the OP) - I did submit a bug ticket and after explaining how this should have worked to the somewhat clueless support people, they "informed the dev team" and gave me refined dil ore for what I was shorted from my Red Alert missions.
From the dev tracker: Red Alert! We'll be shutting down the Upgrade Event to make an emergency fix to the system. We will update you with more info ASAP. Thanks for your patience everyone! How long until October 14? Two weeks? Tick tock, tick tock .....