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Although you will lose some bacteria when removing your gravel, you still have lots in your filter media and on other tank surfaces. You should be OK removing it all at once.

If you have a spare tank you could toss the gravel in there until you confirm by testing the tank with the new sand for a week or two.

If you have any problems you could add back a bag of gravel.
 

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During the change you will turn them off. After the change...that should be plenty high enough unless your sand floats around the tank constantly. I usually try for no more than 3" off the substrate.
 
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