It was in that house____he used to live_____the secret meeting was held.

这里用that是固定搭配 强调句式
it was ……that it is ……that
强调句式的特点就是有它意在强调 没有它句子也成立
It was in that house where he used to live that the secret meeting was held.去掉强调句式为
In that house where he used to live the secret meeting was held.语序更改一下就是
The secret meeting was held in that house where he used to live.句子仍然成立.
而where是不可以的 首先,破坏了强调句式的固定搭配 其次 如果用where这个句子没有主语,本身是不成立的.