*Change* is an ergative verb:

1. As an intransitive verb, its subject undergoes the change:

  > The English language has changed over time. 

2. As a transitive verb, its object undergoes the change:

  > **Someone** has changed the English language over time. 

   Now we have ***someone*** causing the change.

3. And when you passivize the transitive version, you end up with your ***been*** sentence:

  > The English language have been changed over time <strike>by **someone**</strike>.

   We still have *someone* causing the change, but the ***by someone*** phrase has been omitted.

So although both sentences work, the ***been*** sentence implies that it's been changed ***by someone***.  And that's not really how language change works, so the sentence isn't really true&mdash;though it *is* perfectly grammatical.

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You also ask about three sentences:

> 1. How the English language has been changed over time?
> 2. How has the English language been changed over time?
> 3. How has the English language changed over time?

We've already covered the difference between sentences 2 and 3, so I'll just talk about sentence 1.  This sentence has the form of an interrogative clause, but main clause interrogatives are usually marked by **Subject-Auxiliary Inversion**.  This isn't, so it doesn't work as a complete sentence (except as perhaps an echo question or the like):

> how [the English language]<sub>*subj*</sub> has<sub>*aux*</sub> been changed over time

It does work as a subordinate interrogative clause:

> I wonder [how [the English language]<sub>*subj*</sub> has<sub>*aux*</sub> been changed over time].

It works as a complete sentence if we invert the subject and auxiliary.  If we do that, we end up with sentence 2, which is perfectly grammatical:

> How has<sub>*aux*</sub> [the English language]<sub>*subj*</sub> been changed over time?

Though note, as previously discussed, that this question implies it's been changed ***by someone***, which doesn't entirely make sense.