At a daf shiur where I am a sometimes once a week substitute I was asked the following question: how can the gemara (Zevachim 58-59) have a machlokes Tanaim whether the mizbeyach stood in the north/south/center of the Mikdash? These Tanaim did not live so long after the churban and they might have personally seen or known people who had personally seen the Mikdash while it was standing. Didn't anyone remember?
Granting the premise that the memory of where the mizbeyach stood would remain fresh in at least some people's minds (which I'm not 100% certain about, but it seems reasonable), I proposed two responses:
1) Where the mizbeyach stood last time around is irrelevant. If in theory the Tanaim agreed to darshen pesukim differently and locate the mizbeyach in a different spot, that is what we would do going forward.
2) As we once discussed, the metziyus is not necessarily proof in the world of halacha. R' Dessler points out (Michtav m'Eliyahu vol 4 p. 56-57) that we have disputes in many areas where it is inconceivable that there was not some historical precedent or even some common practice that would support one side over the other. Yet, that proof does not make for torah sheb'al peh. Halacha can only be derived from derashos, from a mesorah, from sevara. Without those theoretical underpinnings, what was done in practice might be called a minhag, but it lacks the formal stamp of law. (I think R' Dessler's chiddush sheds light on a Ran at the end of R"H. The Ran asks how the gemara could have a dispute as to what the sound of a teru'ah should be -- didn't people blow shofar every Rosh HaShana? The Ran answers that all the various opinions -- shevarim, teru'ah, shevarim-teru'ah -- were done in practice, i.e. they were minhagim, but the gemara wanted to codify a standard, i.e. codify one view as a matter of law.)
On a similar note (not exactly the same): Chazal teach (Ta'anis 5) that Ya'akov Avinu did not die. The gemara asks: but we know that Ya'akov was embalmed? To which the answer is given that our teaching is based on a derasha. Everybody wonders what kind of answer that is -- so what if it's a derasha, it still contradicts reality!? R' Chaim explained that if "Ya'akov Avinu lo meis" is a metziyus, if it is based on an observation of reality, then it can be challenged and disproven by a contrary observation. However, if it is a dersha, the facts on the ground can't stand in the way. OK, so we have a question from what we see as reality, but that proof is not strong enough to force us to dismiss the equally strong reality of the truth of the derasha. (Something to keep in mind when dealing with other areas like this...)
So much for my 2 cents. Anyone have any other ideas on how to answer this question?