First time building a rig and, like a bonehead, I oriented my Arctic Freezer in the wrong direction initially. I pulled it off and replaced it in the proper direction, but do I need to reapply the thermal paste?
They say that you get air bubbles if you don't. You might take some temperature readings and then reapply and take the same readings. I have yet to see anyone post real-world numbers proving that removing and reapplying the HSF raises temperatures.
As long as you're using the MX-1 thermal compound that comes pre-applied to that heatsink, I wouldn't worry about it. It's not at all prone to air bubbles, like some compounds are.
edit: That would assume that you didn't run the system, before removing it, though.
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