Are there formal mechanisms in any Buddhist institutions that explicitly reconcile Buddhist principles with science? If science proves some belief of Buddhism wrong, then Buddhism will have to change. In my view, science and Buddhism share a search for the truth and for understanding reality. By learning from science about aspects of reality where its understanding may be more advanced, I believe that Buddhism enriches its own worldview.
  -- Tenzin Gyatso, the 14th Dalai Lama in "Our Faith in Science", The New York Times


This is all very well, but are there formal mechanisms in any Buddhist institutions that explicitly allow Buddhist principles to be reconciled with the findings of science?
The general claim in Buddhism, or at least in Theravada Buddhism, is that a Buddha is omniscient. That makes it difficult to question what the texts claim the Buddha himself said. In a couple of places this seems to put science and Buddhism at odds (e.g. causes of earthquakes).

The closest we have to what you are suggesting is an act of the sangha; after the Buddha passed away, we have record of a Buddhist council where they discussed whether to revoke the minor monastic rules as the Buddha had allowed them to do, and they decided as a group not to. Later sangha councils edited the canonical texts but would never have redacted something that they thought the Buddha had said in error.

I think, at the very least, unlike faith-based religions, Buddhism doesn't rely on absolute statements of truth, but rather practices that lead to self-realization; so it doesn't matter as much if statements in the canon like the causes of earthquakes and the size of the universe, etc., are accurate. What matters is if the path leads to the goal, and that is to be verified by oneself.

As a result, you find more marginalizing of problematic teachings, rather than striking them out. First of all, because the Buddha was said to be infallible, but second of all because we know that we are not. The fear of wrongly striking a teaching out of ignorance is too great. But, we can always ignore troubling passages, I guess similar to how Jewish people ignore Leviticus for the most part.

So, no, there isn't really such a mechanism, afaics.