Learn English – Which is correct, and why? “My friend hasn’t / hadn’t been in church in two weeks”

The difference between these two is actually that the "didn't" version is what is called the simple past and the "hadn't" version is called the pluperfect. In practice, particularly in informal English, there is very little difference between the two and many native speakers will use them interchangeably.

The difference between the two is that the pluperfect emphasizes that the action you're talking about (closing the window) happened before the other thing you're talking about in the past. It could be used to contrast that afterwards (when you noticed it was cold), you closed the window, whereas the simple past very slightly infers that the window was still open even after this.

Pluperfect:

"The living room was cold, because we hadn't closed the window; so I closed it and lit a fire in the fireplace."

Simple Past:

"The living room got wet in that storm, because we didn't close the window."

Another possible distinction between them is that "we didn't close the windows" could be taken to mean a "habitual" action that was true of this past time (when you were cold): that is to say that at this time you are speaking about, you commonly left your windows open, and thus the room was cold. "Hadn't closed the windows" doesn't carry that same potential meaning.

An example of this usage:

"When we lived at that house on Smith Street, the living room was always freezing cold, because we didn't close the windows!"

All three sentences are colloquially correct when spoken, and totally unambiguous. B would sound more formal because of the words "has been", but otherwise their meanings are all the same.

However, C is the only one which is correct in writing. The phrase "since I have done this…" is (I think) only properly correct when the word "since" is interpreted as "because", as in "Since I've eaten this pie, I'm not hungry any more". It sounds a bit clumsy even in this context.

Personally, in writing, I would prefer to mix B and C:

It has been two weeks since I (last) saw you.

And in speech, I would contract "it has":

It's been two weeks since I (last) saw you.

In speech and informal writing, the word "last" could optionally go at the end instead, but it reads a bit oddly in very formal writing:

It's been two weeks since I saw you last.