In a clause, which is correct, が or は？

Question

は　means the main focus is the thing after it.

が　means the main focus is the thing before it.

1. それは何ですか

2. 何がそれですか

This is my understanding about one of their many differences. I wonder if this difference is gone when it comes to the subject of a clause. These both mean "I don't know what it is," right?

私はそれが何かわからない

私は何がそれかわからない

More examples:

お兄さんがいつ戻っているかあなたは知っている？
Do you know when your brother will come back?

私はだれが窓を割ったのか知っている。
I know who broke the window.

が is used in these examples. Should I always use が in a clause, or I can use "は" also?

(Since I have definitely seen は being used in a clause, I would like to know if that is just spoken Japanese or something. Is it appropriate to use it like that in formal writing?)

Answer 1

First, I'd like to correct the themes.

は means the main focus is the thing after it.

が or other case particles put in a prominent position in the main clause of a sentence mean the main focus is the thing before it.

In other words, this feature is lost in sub clauses. So, as you say, 何がそれかわからない and それが何かわからない are the same, though the former sounds somehow more emphatic. (In other words, が can't simply stand for the subject in a sentence of statement.)

As for your latter question,

1. お兄さんがいつ戻っているかあなたは知っている？

Even if you change お兄さんが to お兄さんは, it still makes sense and is natural whether the likes of it appear in writings or conversation though it becomes obscure if the お兄さんは is a part in the sub clause or apart from it and sentences may be disproportional depending on how you compose them.

2. 私はだれが窓を割ったのか知っている。

You can also say 私は窓は誰が割ったのか知っている, though the same problem of 窓は's obscurity arises again.