Ok, let's take a step back. Put those two cars out of your mind for a minute.
Here's what's supposed to happen normally, train #2 comes through in the wee hours of the morning and drops off 1 sleeper and 1 coach for the Texas Eagle. Crews over the next few hours switch those cars onto the Texas Eagle consist that had arrived the night before, getting the train ready to head to Chicago at 7:00 AM.
Obviously in the other direction, the opposite happens with the Sunset picking up the cars dropped by the Eagle.
Now, the two cars that are always there only come into play if #2 is running so late that it won't arrive into San Antonio after 7AM. If that's going to happen, then the yard crews take those spare cars and put them on the Eagle to make up for the two cars still stuck on the delayed Sunset.
This allows Amtrak to honor reservations made along the Eagle's route in those cars. Without those spares, Amtrak would have to deal with disappointed customers along the way who don't have a seat or room. Additionally, if the Sunset isn't super late, read still in Arizona, then Amtrak will take those through passengers off the Sunset at an earlier stop and bus them to Fort Worth to connect with the Eagle and of course those spare cars provide the room for those bused passengers.
Now, eventually the Sunset gets into SAS and just like normal, it drops off the two through cars for the Eagle. Since the Eagle is long gone, those two cars now become the spares for the next time.
Finally, as I noted earlier, if either the Sunset or the Eagle comes into town with a car giving them problems, then that car would be cut out of the consist and the appropriate spare would be cut into the consist.