When we read the original sentence, we should note it had been is in the past perfect tense, which should only be used to describe action that is completed earlier than some other past action (expressed in the simple past tense). Since the other action (can reconstruct) is not in the past tense, the past perfect is incorrect.
Therefore, choice (A) is incorrect.
Choice (B) is incorrect because it uses the present perfect tense (have been) and introduces the hypothetical might. The author isn’t trying to communicate that the paleontologist might reconstruct a local ecosystem as though the paleontologist might never know for sure.
Answer Choice (C) is correct because it uses the simple past tense to describe a past condition.
Choice (D) is incorrect because of the introduction of the awkward expression as if and the use of redundant during a time. During indicates time.
Choice (E) is incorrect because the use of though introduces a hypothetical element similar to choice (B). The pronoun it also doesn’t have a clear antecedent (the word the pronoun renames).