Algae problems can come from the sand, but it's all variable. Detrius can build up in a deep sand bed, and pockets of gases that cause havoc when released. Having a good cleaning crew, nasarius snails, conch, sand sifting star fish, and gobies help take care of that. Removing your sand bed, or lessening it, will release problematic substances into your water column. This can be taken care of through water changes and if you take care when removing it.
But now about me. When I bought my tank, used, it came with a good 4 inches of sand bed. I decided this was causing issues and siphoned out all but about and inch. I regret that decision now, I wish I had about 2 inches. So, go slowly and make sure you save your old sand, you may want it back some day.
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