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Controlling video card fans

I have a loud video card that I need to control with a fan controller. The connector on the fan, however, is a 2-pin small connector. When I shove it onto a regular 3-pin connector hooked up to my fan controller, it controls and works just fine.

Are there any adverse affects as a result of this, or can I just tape up the odd physical connection and leave it in there?
 
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