I don't know if my situation is totally analagous, but I was involuntarily rebooked from AA to UA for my outbound this past summer due to schedule problems.
UA was happy to give the miles, although they refused to apply any bonuses since my ticket was originally from AA, even though I used my best legal skills to explain to them that someone somewhere had paid for the ticket and it wasn't like UAL let me ride for free! AA only gave me miles for the AA flights I had missed after about an hour on the phone with AAdvantage CS; I was told that it was not normal policy, but since I hda had several problems with AA on my trip, they were extending me a special courtesy. Don't know how this works the other way around.