The Diary of Anne Frank tells the true story of a young girl and her family that were hidden during the Nazi occupation of the Netherlands by a gentile Dutch couple, though they were eventually discovered.

A. that were hidden during the Nazi occupation of the Netherlands by a gentile Dutch couple, though they were eventually discovered
B. that were hidden by a gentile Dutch couple during the Nazi occupation of the Netherlands, though they were eventually discovered
C. whom a gentile Dutch couple hid during the Nazi occupation of the Netherlands but were eventually discovered
D. who were hidden by a gentile Dutch couple during the Nazi occupation of the Netherlands but were eventually discovered
E. who were hidden by a gentile Dutch couple during the Nazi
occupation of the Netherlands even though they were eventually discovered.

Source: ManhattanGMAT SC Test

OA given is D. I agree with OA but my doubt is about the "but" in option D.'

I read in most of the questions that the "conjunctions are used to connect two independent clauses." "But" is one of the conjunction. So, in option D "but were eventually discovered" is not an independent clause and so doesn't seem to follow the rule. So, please explain why the usage of "but" in this case is valid.

Thanks!

GeeMate.

What I understand of the SC given, though I agree with you, the usage of "BUT" is to bring out the exact meaning of the SC, The meaning of the SC says the "FAMILY was hidden,BUT later found", so BUT is used to contract.
The other part is the // of the SC words like BUT, AND , OR it will follow //, so you need to pick a SC option which has "were"(for this SC) after and before BUT, other options, // has to be maintained

When do you use whom and who?

Who refers to the Subject of the sentence
whom refers to the object of the sentence,

This comes under ellipses part of it. So the sentence is actually,

The Diary of Anne Frank tells the true story of a young girl and her family who(Here who refers to girl and her family) were hidden by a gentile Dutch couple during the Nazi occupation of the Netherlands but [who] were eventually discovered.

Since the second who is obvious, it has been omitted. Consider this sentence:
"I like books and chocolates". Here "and" too is a conjunction but that doesn't make chocolates alone an independent clause. When you disect this sentence, it will actually be,
"I like books and [I like] chocolates.

Regarding who vs. whom, somewhere either in beatthegmat or manhattangmat, Stacey has given a nice explanation. Will drop the link if I can find it.

that's a vast overgeneralization; clearly conjuctions don't always have to connect two independent clauses. if that were the case, then "and", also a conjunction, would be wrong in any other case - so, for instance, it would become incorrect to say i bought apples and oranges.

"but", like "and", can connect many different types of parallel structures.
this course is difficult but enjoyable.
james finished the first stage but was too tired to continue.
etc.
(it can also be used for two independent clauses, as you've said - but it certainly doesn't have to.)

"who" is a subject pronoun. if you'd use he/she/I/we/they (other subject pronouns) in the same situation, then you use "who".

"whom" is an object pronoun. if you'd use him/her/us/me/them (other object pronouns) in the same situation, then you use "whom".

by the way, this will almost certainly not be tested. it has shown up in a grand total of 0 official problems to date. (note that you can't split on it here, either.)

--

also:
for extremely general grammar questions like this one, you are MUCH better off just conducting a random google search. (try typing "who vs whom" into google - you'll get thousands of results.) those pages will give you a much more complete treatment than we could in a single post.

for specific questions pertaining to particular problems, though, this is the place to be.