By ‘indices’ he refers to work through connection with, or cause and effect of, the thing to which reference is made.

网友把 By ‘indices’（借助索引），理解为 is made 这个动作的施事者（主动语态的主语），所以把它放在句末。即：

He refers to work through connection with, or cause and effect of, the thing to which reference is made by ‘indices’.

首先说明：By ‘indices’放在句首，它一定是修饰主句的谓语动词（refers to），说明refers to 的方式，不可能瞒山过海去修饰一个定语从句的。从结构上即可判断出来，这不应该有争议的。网友理解失误。

through connection with, or cause and effect of, the thing... 两个介词共有一个宾语 the thing。

through connection with, or cause and effect of, the thing...  等于：

through connection with the thing or through cause and effect of the thing

我根据颜色英汉对应翻译：

By ‘indices’ he refers to work through connection with, or cause and effect of, the thing to which reference is made.

【翻译】借助“索引”，他指的是通过与所指事物的联系或因果关系而进行的工作。