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Yes, contamination can occur, but it's minimal. best to do this service while also doing an oil change. Bleeeding the cooling system would be another best practice. When all buttoned back up just run the electronic procedure. Turn car to on position, put heat to full, hold down gas for 10 seconds, and let the electronic pump do its thing for roughly 10minutes (dont open/close doors as it will interrupt the bleed process).
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