Yes, I did. They confirmed that the ticket had been cancelled but I can't request a refund yet "because the computer hasn't caught up." Very polite and helpful, but recommended that I try again tomorrow after the 24 hour window has elapsed.
I'd be stressed too but if several segments just did not ticket I doubt you are expected to pay for the segments that did.
My experience with the online refund thing months ago is it is quirky and multi-step. Can't really remember my full issue after a weather cancellation (rebooking offered but got me there too late to save the trip). I just remember getting frustrated with a balky online system and having to call them to fix it--even after the systems finally caught up and got in sync.
American Express advises me that, if I am going to need more than 24 hours to request a refund, I must get an e-mail from AA saying that this is ok and due to computer systems malfunction. Otherwise there is nothing AmEx can do for me if AA won't refund the ticket price to me because I did not request it within the 24 hour window. Not too helpful, but at least AmEx is being honest!
Does not really sound like Amex, but, I'm guessing the charge is still in the pending stage. Most charge backs cannot be done before charge is final or even the billing cycle is closed. The conversation sounds premature, especially if you have the documentation saying segments did not ticket.
I feel your pain but predict this will fix itself.