Depending on the legth of downtime SE's are not a problem unless you are down a prolonged period, I've seen literally a week pass and there were no problems. That may be affected by the trust the SE puts in your site.

I agree with crankydave you want to have both sites running at first as intenet domain records are cached on some servers longer than others. I generally try to give it at least two weeks. I also use a live/development sites setup so if there is a malfunction or problem you can roll back easily by just flipping a switch. That makes a rollout or update less stressful.

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