1 Tom’s father died on May 1st, but the day before then he had looked pretty well.

此句中的then不是指May 1st, 而是指that time，即the time Tom's father died. 即时间副词then指代的是前一个分句谓语动作发生的时间。

Tom’s father died on May 1st, the day before when he had looked pretty well.

改为定语从句结构后，when取代了then, when的先行词是主句内容，而不是May 1st.

2 My uncle works on a farm, and in front of it there is a lake .

这个句子中的人称代词it指代farm。

My uncle works on a farm, in front of which there is a lake .

改为定语从句后，which取代it，which的先行词为farm。

这就是你问的问题的原因。第一个定语从句修饰主句。第二个定语从句修饰farm。