I was on an American Airlines flight out of Dublin that was completely canceled and rebooked to British Airways. At the time, elite miles weren't available on British Airways, which was the entire reason I chose to fly on American.

I called Alaska and they told me there was no way to get credit for my original flight. Once I got home, I wrote them a letter and included my original itinerary and the American Airlines miles posted a couple of weeks later instead of the BA miles.

You may want to try writing a letter once you get home.