Think on a drain refill there is only 4.5-5 quarts in an auto trans, so you replaced the majority of it

 

Here is the reasoning I have which appears to make this whole thing confusing.

1. The trans hold 3 quarts and the torque converter holds 12 quarts.

2. The fluid from the trans and from the torque converter both flow into the trans cooler and are mixed together in the trans cooler.

3. If 2 is true, the fluid in the torque converter must be brown if the fluid in the trans is brown. When 3 quarts are changed in the trans, 3 red quarts mix with 12 brown quarts causing the 15 quarts to be brown. Maybe not as brown as before, but still brown.

4. If 2 is false, the trans is not cooled by the trans cooler, only the torque converter is cooled by the trans cooler.

The fluid in the trans has not gone dark again even after about 500 miles. This indicates 2 is false, but I have always thought the trans cooler cools both the trans and the torque converter.