I agree completely with what Toad37 said. You want the heat correct at the bottom of the tank. If the discrepancy is dramatic, as in your case, you might have too much substrate and can fix that by removing a little.
In general, if the substrate is too thick it can lead to bacteria buildup and mold, etc. if the tank is humid.
I am not a substrate expert but you only need a thin layer of most substrates.
Just a thought.
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