AA can definitely vacate the seat assignments if they sub in a different aircraft. Doesn't have to be a different type; if the tail number changes the system will start all over again.
Another thing that will cause AA flights to scramble a large percentage of the assigned seats is deadheading. Company policy is that deadheading air crew are always seated on the aisle, and they may decide to put aircrew on the flight within an hour of boarding. The system will always reassign other passengers to put aircrew in aisle seats up front and near the exits.