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He said you could paint as long as it could be painted over, but you didn't leave it as original, so he's charging you to return it to the original color. That charge I can understand. He allowed you to make the modifications, but the implication is that it would be painted over. Since your didn't do it, he's going to. The carpet, however, is another story. He can charge for depreciation (or not at all if it's old enough, depending on the rules in your state).