08-09-2011, 07:26 PM
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Substrate change is best done at one time. Remove everything, wash and add the new substrate, fill with fresh water, use a dechlorinator. Move as much hardscape from the existing tank as you can, even if temporary: fake plants, rock, wood, decor. Keep these under water (a bucket of water from the existing tank) untill you put them in the new tank (after dechlorinating the water). Same with the filter, keep it running if possible and move it over without rinsing the media. The fish will have to go somewhere, like a spare tank, if the filter can be placed in that it will work fine.
If you had live plants this would not be an issue, but none are in your existing tank data. This is a case where I would use a bacterial supplement. Seachem's Stability or Tetra's SafeStart.