Other airlines handle it ok. Have a booking for A-B-C and want to change it to just A-B and drop C, if availability only exists for A-C via B and not A-B on its own, the change cannot be made ( other than rebooking into a different available booking class)

I would be surprised if AA was unable to handle it and the OP of this thread has indicated that he has been unable to make such a change

It isn't as if married sector availability is a new concept

Auto deducting miles for failing to board the last sector would be an interesting approach for the airline to take