Booking multiple Flights at Same Time
 

I am currently scheduled to fly DCA-PHX, departing at 5:05PM and arriving at 8:28PM. I then need to fly PHX-SFO, and the flight I would like to book departs at 5:47PM. I am unable to change the DCA leg (I'm the main traveler, and I used a companion pass for a friend). My hope is to do a SDC or SDS to an earlier flight out of DCA, arriving in time to catch the PHX-SFO flight.

Will AA allow me to book the desired flight at the same time? Or do I need to remove the FF number from my reservation when I book? Will I run the risk it is canceled by AA due to a multiple booking? The only other option is to book on SW, but obviously, would much prefer AA.

Yes, it will be no problem at all to book the 5:47p flight from PHX. When you book it just make sure you ticket it and don't just put it on hold. It's the on-hold reservations that AA's system will auto-cancel if it thinks it's a duplicate or overlapping booking.

Does it matter if I include or omit my FF number then?

Doesn't matter, no problem to include your AA# on the new booking as well.

While less common, there are certainly known instances of AA cancelling duplicate reservations even after both are ticketed.