When I encountered a similar situation earlier this year, American cancelled the ticket and gave me the ticket number, so that it could be applied to future travel with the understanding that the change fee would be applied at the time of new booking AND I would have to call to apply the credit, since they did not have the capability to do so online. I had a year from the original date of travel to use the credit.

When I called to re-book after placing a ticket on hold through AA.com, they took the change fee out of the original credit and applied the remainder to the new ticket. They did not charge me the phone reservation fee though.

Hope this helps.