Short answer: I doubt it will change the outcome.

Long answer: That is how I would do it. Flush out what you can to get fresh fluid in there. Then drop the pan, do the valve body and solenoids and replace the filter. You will lose a couple L of fluid in the pan doing it this way though.

On the other hand, the direction of flow would be picking up fresh fluid directly through the filter after the pan drop, so even if you did the flush at the end, the filter and pump would really only see clean fluid anyway. This way would be more efficient in time and save some fluid.

 

From the horses' mouth.