What is a good way to understand this sentence in my lease?
No; in very simple terms, you place the $1000 as a sort of 'trust' fee; that means that if you decide not to do whatever you intended to do, that fee is not returned to you. However, if you fail to meet with your agreement and you still want to do it again, then yes, you will be required to pay another $1000 as a security deposit.