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The more panels you remove from the rack, the less control you'll have over the airflow. Rack mounted equipment is generally designed to have a specific airflow direction, and when setting up a rack and choosing gear, one of the considerations (often ignored) is to verify that all your components that will be sharing the rack have the same direction of air flow. If you have back-to-front gear mixed with front-to-back gear, essentially you have created a thermal feedback loop.

The consensus in the thread so far is to leave panels in place, and I agree wholeheartedly. The next question is the direction of airflow of your components, which will tell you which way you need to move air through the top of the rack.

If your airflow through components is front-to-back, the the top fan must move air out. If component airflow is back-to-front, the top fan must move air in.
 
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