I lost all the fluid in my trans one time and it took a lot of driving to purge the sytem fully. I also thought I blew my trans.
When in drive the trans would go automatically in to 5th but I had reverse. I drove around in reverse to purge the system of air and heat up the fluid. Finally as the trans got some heat in it, it started to shift in drive, still erractic but better. After I got a few foward gears I got some more heat in it and the more I drove it the better it got and soon after it was normal. Shifting threw all the gears like it should.
I think the trans has to be at a normal operating temp to open up the all the valves in the valve body. Then you will be able to purge the system fully.
Remember to keep adding fluid as the trans purges the air, just try and not overfill. Also when doing this dont abuse it as it could lead to some other issues