The only problem I see with stirring up everything in the tank is all the little nasties in your sand now will become part of the water column possibly throwing your water out of wack. In my opinion I would think you would want to put the new sand on top of the old disturbing the old sand as little as possible, there will prolly be a little die off but I wouldn't think this would cause as many problems as stirring the old stand. This is all just my opinion and I would wait for verification from some of the other board members before I went ahead with anything.
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