I just had a problem like this happen last week where I was routed BOS-ORD-MAN (purposefully for extra miles) but my BOS-ORD got cancelled and they put me BOS-MAN nonstop. I just received messages from AA as I was in a meeting and by the time I called back they had already rebooked me on the n/s. I puyrposefully asked the EXP agent if I would be able to get original mileage credit and to note on the reservation involuntary reroute and he said that the original mileage credit woudl be no problem.
I called this morning to inquire about getting the original mielage credit to post and the very nice AAdvantage CSR who helped me said taht it is against their policy to give original mileage credit and that the EXP desk is wrong to give a blanket answer that they will. I then told her he put a note in my file regarding it and that I would have asked to been rebooked via ORD had I known this. She eventually did credit me the original miles but said that it was a one time thing. I had never had to do thsi before and I was just curious as to whether it is just a YMMV or if this was the actual policy?