I had a similar situation back in September, using AA web special as a backup several hours after my original flight on Delta. I never checked in for the AA flight and only had carry-on bags. Once I knew my Delta flight was departing in time, I canceled the AA award on the AA app and it immediately refunded the miles. The $5.60 refunded to my credit card a few days later.

As long as you have a seat assignment, you shouldn't have to check in on AA until you know you need to take the flight. I'm not sure if AA allows cancelation of award after checkin but before departure. Might be a good question to ask them via Twitter.