选前面的是因为which指代了damage,which后面的句子构成了一个从句.
不可以选第二个,选的话你放进去看看,不就成一个句子有两个主谓结构了吗?前面he listed 一个,现在he supposed 又是一个,一个句子是不可能出现两个主谓结构的,
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in his report he listed the damage __ had been done by the terrorist attack.
(1)which/that had been done
(2)he suppose 可以看做插入语