The transmission flush usually involves some kind of a cleaner going into the transmission to dissolve varnish and to dislodge the buildup of particles. As the transmission works, the gears touch one another and wear small particles away and those collect in the crevices and nooks in the housing and pan.
Whereas if you were to get a fluid change, this means the old fluid is removed and new fluid is replaced.
There can be two different types of fluid changes: One is where the bottom of the transmission is opened, the fluid is drained out, and the filter is replaced. The second type is when a machine is connected to the "cooler lines" (explained in more detail below) and All the old fluid is exchanged for the new fluid.
Some transmissions may have a small radiator that is located near the engine coolant radiator. The fluid from the transmission circulates through lines and goes from the transmission to the radiator and then back to the transmission; it helps to cool the fluid.
When the bottom of the transmission is opened and drained, there is still a lot of fluid in the inner passages and torque converter of the transmission- so not all of the fluid is changed out.
When a flush is performed, the old fluid is removed from the "cooler lines" and the new fluid is added through them, so all of the old fluid is taken out.
Bottom Line: I wouldn't flush the car due the seals breaking, other things going wrong, etc that would end up costing you more money. BUT ALSO: Like Nick said, if you've already flushed half of it, might as well flush the rest since you're halfway there :P