Quote:By the time the delegates arrived at the convention center, the international conference on climate had started.
Quote:by the time he got there, the train was long gone.
Though they look similar, these two sentences are subtly different from each other. Both of them describe events that occured prior to other events, but the prior event in the first sentence (i.e. "had started") has a definite stopping point while the prior event in the second sentence (i.e. "was long gone") continues.
"the international conference on climate had started"
This is the first event to happen in the first sentence, and it ends before the second event. That is to say, the act of "starting" happens only once--the conference has only one starting point. The conference started
before he got there, but it was not still in the process of starting when he
did get there.
"the train was long gone"
This is the first event to happen in the second sentence, but it does not end by the time the second event ("By the time he got there") occurs. Notice that in this clause, the predicate is an adjectival description--i.e. the sentence is not telling us what the train
did, the sentence is attributing a
property to the train and telling us what the train
was. This property continues to be true by the time the second event occurs: the train was gone before he got there, and the train is
still gone when he does get there.
Of course, it would be perfectly possible to rewrite the second sentence such that the prior event is an action rather than a property: "By the time he got there,
the train had left." In the case, the sentence is now similar in structure to the first sentence. In fact, I suspect this version of the sentence would be stylistically preferred in formal writing, though it's a close call.