Leaching, the recovery of copper from the drainage water of mines, as

Perhaps I can help clarify the trouble people are having with past perfect ("had been") vs. simple past ("was").

First, past tense does not necessarily mean that something is no longer true. For instance, I might say "When I was a child, I wanted to grow up fast because my brother was so much older than me." This doesn't mean that my brother is no longer older (thankfully, I still have my brother!). I am just talking about him in a past context. It would be wrong in this case to say "is so much older" just because he is still older.

Second, we don't always need to use past perfect when we have more than one past event. We only use it when the order of those events needs to be clarified or emphasized. For instance, we would say "I was born and raised in California," and not "I had been born in California and then raised there." It's clear enough that being born came first, so there's no need to use the past perfect to clarify. In other cases, we simply don't care which came first. If I say "I have studied French, Spanish, and Russian," I don't need to use "had" to show which came first unless the order is somehow important: "I had already studied French when I started to learn Spanish, so I had an easier time learning vocabulary."

Third, if we are going to use past perfect, we must have a clear time in the past that we are placing our action before. If I say "X had happened," I need to say which past event it preceded, or at what point in the past it had already happened: "X had happened when Y came along" or "By 1850, X, Y, and Z had happened." I was initially going to use "X had happened before Y did," but that's a case that's clear enough without past perfect, so it would be better to use simple past: "X happened before Y did." Notice that dropping "had" from my earlier examples reduces their clarity: "X happened when Y came along." (At the same time? After?) "By 1850, X, Y, and Z happened." (This is not as bad, but it makes it a little less clear that all of these things could have happened at any time before 1850, perhaps even many years earlier.)

Regarding this usage in particular, notice that E doesn't provide any reason to use past perfect. The most simple way to see this is that although we have more than one point in time (the 18th c. and 25 years ago), the main core of sentence does not say that leaching was a method before or by one of those times (the modifier does, but it's not part of the action!). It just says "Leaching had been a method, but until 25 years ago," we didn't know a certain thing about it. When I see "had been a method," I immediately want to know "until what?" The sentence doesn't answer that. On the contrary, it makes it seem that leaching continues--we just know more about it now. Furthermore, even if people stopped using this method, it would still be a method of mineral extraction--it just wouldn't remain in use.

Consider this case:

"Cockroaches had been an insect, but last year, scientists learned more about them." What? Cockroaches had been an insect? Did they stop being an insect and turn into something else? When did this happen? This sentence doesn't make much sense meaning-wise, but it also doesn't meet the criteria for past perfect. We aren't situating one past event in relation to another.

When would "had" be appropriate? Try this:

"By the time the first birds evolved, cockroaches had already been flying for millions of years."